Did they kill all giants from the camps around Jorgenfist walls? If not, he waits until Frost Giant tribe comes, and invades lowlands as fast as he can. Starting with Sandpoint as a high-priority target.
Remember that he has a job from K to be done.
Could you elaborate? The pc's have cleared out the "Under Jorgenfist" (Area B1-14?) What does "Conna has been evacuated" mean? She left with the pc's? She doesn't really need to be rescued - she wants to save the stone giants from Mokmurian. She should have made clear that the pc's need to go to the next level down. What is the pc's plan? Why do they think they can leave for a week? And how did they manage to take out the frost giants but otherwise not get entangled with any thing else on the surface?
Mokmurian has some problems - what is he going to tell the frost giants when they arrive and find their ambassadors dead? Is Conna still in Jorgenfist? Does she know what happened below - that's a lot of casualties for M's forces to absorb? If the giants find out their morale is likely reduced along with their opinion of M - how could he let this happen?
He could move more giants and dire bears (perhaps Ember?) into the rooms below but the presence of the haunt and the temple to Lamashtu may dampen enthusiasm. He could also use the Runeslave Cauldron to "revive" the dead stone and frost giants and use them to guard the level - this would keep the other giants from knowing that happened and seeing for themselves just what is Below Jorgenfist. My view is that the stone giants don't care what M does to hill giants but if he starts making runeslaves of stone giants that might not go over well. If it's part of a successful war of conquest - perhaps okay; if it's to restock defenses after defeats, not so much.
Oh my.
I hate to say it but maybe continuing isn't a good idea. If they don't enjoy Jorgenfist, Runeforge will be anathema. Book 6 will be just as harsh. I'm not an expert on all the AP's but perhaps something like Hell's Rebels would be more to their liking?
You could appeal to their role-playing interest - while the players may not care for dungeon crawls, the player characters should be very committed to dealing with Mokmurian and Karzoug, who represent catastrophic, DefCon 0 level threats to all the peoples of Varisia.
But if they don't like dungeon crawls, you're in for a hard slog through the last 3 books of RotRL. I'd say a frank discussion with the players is called for. There are time periods between dungeon crawls/combat zones in the remaining books for the type of role-playing, character developing activity they like but they can't take a week of PTO in the middle of a dungeon.
As for why they thought they could go spend a week away: it's because my players didn't really want to go back.
The heart of the problem is out-of-character. My players just don't enjoy dungeon crawls very much. They prefer the scales tilted towards complex role play and character development, interspersed with occasional light combat.
Our group was in a situation that was a little similar to yours, though my players do like combat. They loved the rich stories of the first parts of RotR, the complex villains and the choices they were forced to make. (I did expand these parts to make them even more central.) But they didn't much care for the shift to more black and white villains and situations in the later parts of the AP and the room-to-room hack 'n' slash that became the norm. After Jorgenfist I warned them that the rest of the AP would continue mostly along those lines - but if they wanted, I could try to add to it and emphasize the story parts as much as possible (the AP suffers from the all too common phenomena of having lots of great backstory that's seldom presented to the players. So I presented it). We decided to soldier on, but with adjustments made by me. Here's a short summary of some of the stuff I added, if you're interested:
I added a segment between parts 5 and 6 in Sandpoint to nail home how Varisia would look after Karzoug's victory. I added some puzzles (based on info from Runeforge) to find the way to Xin-Shalast including a ritual at a giant statue of Karzoug. I took away the Vekkers and their cabin and instead made the whole trip (they had to walk, starved) along the ghost river full with haunts and Leng nightmares. I added more politics and roleplay in Xin-Shalast - I had Conna be there with her tribe, and the PCs had to break her runegiant Dominate for her to help them, and some giant's politics. Also more stuff with getting help from the Spared and their prophecy about the PCs.
Lastly, in the spire, I made it more influenced by Leng and instead of mini-Karzougs I made them encounter ghostly nightmare versions of previous villains from the AP. I had introduced Viorian Dekanti prior in Magnimar, as a mighty paladin, so the PCs made efforts to save her from Chellan (which they failed, btw).
One thing that I did overall that helped was removing many of the speed bump fights. I kept a couple here and there so the PCs could feel powerful, but instead I upped the big set pieces. We're just at the door to Big K now, but so far they've enjoyed it, even though they liked the first parts more.
But unless you adjust it I agree with Latrecis - maybe something like Hell's Rebels would suit your group better. We're playing it next :)
The PCs are definitely committed to defeating Karzoug at this point. And the players, despite not liking dungeon crawls, want to finish. We've already spent four years to get this far, so we've got a lot of sunk costs.
I think I need to just jump the rails and treat it more or less as homebrew from here on in, using the books only as a very loose guide. I've already been planning to break book 5 into a series of mini-dungeons scattered around the holdings of ancient Thassilon, so they can do a session or two of dungeon, then a session or two of role play stuff. If I'm sneaky I might be able to get some role play into some of those little dungeons.
For the problem at hand, perhaps I'll take Ashkar's suggestion -- they get back to Jorgenfist and discover that Mokmurian has departed with his troops. Then I can make the rest of the book about (quickly!) rallying allies and assembling an army to defend against Mokmurian. Some of the Jorgenfist encounters (rocs, harpies, etc) can stay there, which will make clearing out the rest of the place a lot more straightforward.
They could get an urgent summons from the Mayor. Ravenmoor has been razed to the ground by an army of Giants! "Weren't you people supposed to do something about that?!" Refugees are pouring into the lowlands and Sandpoint. Dog and Cats living together! Mass Hysteria! Shore leave has been revoked! Get back to work.
I don't know that there are a lot allies to recruit - military forces in the region are going to be hard-pressed to stand up to an actual army of giants even one as "small" as the couple hundred suggested in Book 4. Maybe M has split up his forces in attacks on Ravenmoor and villages west of the Malgorian mountains, down the Skull river to Ilsurian and perhaps at Riddleport or Kaer Maga. Or maybe he's allied with the leadership of Kaer Maga (or Riddleport. Or both!) and the pc's need to break up that alliance.
Taking his army and marching is a good way to cover up any defeat under Jorgenfist and the giants all want to leave the vicinity anyway. I suggest you have the Roc's travel with the army. Would be cool for M to be riding one.
I just wanted to chime in here to throw some ideas out - not sure how you'd work it with the current situation but...
Jorgenfist:
So your group hates dungeons - get rid of the dungeon - make Coana (spelling... the ally giant) contact them - give them quests to 'win over' each of the different tribes of giants (they all have different ways to impress depending on type) have them form an alliance and win the 'army' over. Let them walk up to big M with the entire army at your back and he challenges your party to 'one on one' or something to save face (and keep the army out of the fight). Dump 90% of the dungeon for the above plot.
Runeforge:
The runelords hated each other - make the infiltration about how to win over the various factions - yes perhaps there is a dungeon (and perhaps a wing or two has no interest at all in being allies) but ancient hatred lingers and the minions of the other runelords would hate to see Karzog get out and claim power when their lords can't/haven't.
The big mountain:
Quest 1 - put the dwarves to rest - this can be played up with a group of dwarves staying at the lodge cabin in the woods style that beg for help.
Quest 2 - free the yeti enslavement (roleplaying etc)
Quest 3 - ally the dragon
Quest 4 - free the giants from corruption
Quest 5 - stealth through the fortress of Big K
Quest 6 - enter the final fight.
etc.
There are ways to make the entire thing friendly to your group - however it's going to take a ton of work from you - remember combat is never a 'must' and the only reason there are so many combats is because it takes that many to level up - if you level up by fiat you can eliminate 90% of the combats and keep it streamlined.
And for a future campaign, I might suggest Hell's Rebels. There is a lot more social and diplomatic elements to it than dungeon crawling.
If you want to finish the AP you could of course fast track it.
For example, cut down on the travel by putting the portal to Runeforge under the cathedral of wrath (and remove both Arkhryst and the Scribbler).
In Runeforge, have more sections than Envy be destroyed in the conflict - maybe only two or three factions are left - say, Greed (play up Ordikon's madness for roleplay), Lust (roleplay) and Wrath (could become allies since Alaznist wouldn't want to see her archenemy rise before her). In fact, you could have most of Runeforge work with the PCs instead of against them.
Present information that Karzoug will be much weaker as long as he's not released, and plant research information about the Leng portal in the Greed section so the PCs know that K will get his old armies back when he's released, to give them a sense of urgency and impending doom. Lastly, if you want, you could have the Runeforge itself create a portal to Xin-Shalast by having opposed weapons (i.e. dominant) destroy the statue/golem of Karzoug.
Place the PC's at the foot of the spire, have the dominant weapons work like Sihedron rings against the occlusion field, and make the opponents in the Spire fewer and weaker. Give the weakened Karzoug a couple of permanent neg levels (maybe he's still semi-translucent), get rid of the giants and you're good. Have the flood of angry released souls from the runewell destroy Xin-Shalast and the army there, and make the volcanoes explode for a cinematic ending where the PCs have to teleport away amid falling rocks and lava streams.