I'm hoping that some other GMs can provide their input on my current situation, and offer suggestions as to how to go about things (or if you think I'm doing okay with this).
Due to our game being just a once-a-month thing (some of my players drive for close to three hours to join us, or we use Google Hangouts if they can't make it), I try to give each session a sense of closure and progress, so that they're satisfied with what has happened, and leave them wanting more next time.
One of my players, playing Tordek Hammerfist, an elven Paladin of Abadar, was interested in redeeming Nualia. We discussed it at length, and these forums became incredibly helpful in creating that part of the story. However, he only had about an hour and a half left before he had to leave for his long drive home, so I decided to let Abadar give him a couple of hints as to where to go. This required Wisdom checks with DCs of 20 for Tordek to get the hint of left, right or straight at certain points.
So, they reached Nualia pretty quickly and easily, and then the party's diplomat, Willo (half-elf cleric of Desna), rolled a natural 20 on her Diplomacy check to talk to Nualia.... and I rolled a 1 in front of the players. Yes, I know that a 1 on a skill check isn't an automatic failure, but they had been working towards this for months, quite literally, so I gave it to them. Nualia broke down into tears, and surrendered herself peacefully.
Carl Jenkins (human magus) claimed the Sihedron medallion when Nualia surrendered herself, because his family can be traced back to ancient Thassilonia. His father strongly discouraged the use of magic, while his grandfather secretly trained him in the arcane arts and told him legends of the ancient times. I'm looking forward to his face-heel turn later....
Anyway, the result of this is that Bruthazmus, Orik and Lyrie were never encountered by the players. They want to come back to Thistletop next session and finish clearing it out, while Sheriff Hemlock has Nualia transported to Magnimar for trial.
Here is what I'm thinking: Orik has cut and run. I'll use him later in the story as a somewhat helpful NPC, possibly as a blacksmith or farmer, but he's done with adventuring. Bruthazmus, having no major competitor, is going to presume that he's the new "ruler" of the goblin tribes based out of Thistletop. He'll be there when the PCs return, so that they have him to face before possibly finding their way to Malfeshnekor. But Lyrie....
Two of the other PCs, Nina (human rogue/ranger) and Ganome (gnome barbarian/rogue) were a little rough on Tsuto. They actually tortured him for information, until Tordek interrupted them and forced them to stop.... and then, they "accidentally" killed him.
And burned his body.
And scattered his ashes into the bay, to make sure he wasn't revived.
Lyrie, sometime after fleeing Thistletop, will have learned of their mistreatment of her love, and wants revenge. My plan is to have her be in Magnimar when the PCs go there - I'm allowing them to testify at Nualia's trial before Justice Ironbriar, which will be timed for roughly when they'll be there anyway for the Skinsaw Murders - so that she can, with the help of some Skinsaw cultists and a few hired goons, attack the party and attempt to assassinate Nualia.
One of those goons in particular is tied in with Nina's backstory, but that doesn't really apply to much of what I'm discussing here.
Ultimately.... does all of that seem plausible? Do you think it works, or are there points of the larger story I'm missing?
That all seems perfectly reasonable to me.
Why would Lyrie want to assassinate Nualia? Seems like a difficult thing to do for no obvious benefit.
Might I recommend taking a look at The Lyrie Scenario.
You could easily turn it around into a set up by Lyrie to learn their secrets then lead them into the ambush.
I had a lot of fun with it myself and could easily see having gone WAY different with Lyrie having a different set of goals.
The only thing I would question is Bruthazmus. He doesn't strike me as the type to stick around and be leader. He has preferred to hunt alone and take Elf-ears where he can. That might change based on having Ripnugger's harem to himself... but it seems like if that's what he wanted, he could have done that earlier. So it seems out of character for him.
That leaves two basic reactions. One, he is determined to save Nualia from her fall and restore her to Lamashtu's service... or, two, he is enraged by Nualia's betrayal of Lamashtu and wants to destroy the party that caused it (and probably Nualia herself as well). Being the lone hunter type, I don't see him joining Lyrie's plot.. more likely, he would try something on his own, like ambushing lone PCs while they travel between Sandpoint and Thistletop. Add the Trapper archetype to his Ranger class, and there's a lot that could be done with that.
Random thoughts...
First, another thread in desperate need of spoiler tags.
Second, don't see anything "wrong" in the OP's write-up. In some ways Book 1 is the most flexible in the AP.
If the pc's get connected to Sandpoint, prevent it from being overrun with goblins and meet Aldern, anything else is gravy.
Third, a few questions...
Why is a paladin tolerating companions that murder prisoners and make them unrevivifiable? (Which arguably is another crime in and of itself in a world where resurrection is possible.)
Echoing Mudfoot, why is Lyrie after Nualia? Shouldn't she be after the pc's? And remember Orik is infatuated with her - he might follow her and support her plans.
How is giving Nualia over to Ironbriar and a trial "redeeming" her?
RE: spoilers, one of the things people need to remember is that the title of threads appears in the "Messageboards" sidebar on the main Paizo page. So something like this thread, with the title "Nualia's accomplices escaped" could very well spoil someone playing in the early stages of Chapter 1 (because Nualia is assumed to be have died in the chapel fire) even if they're disciplined enough not to go to the Rise of the Runelords sub-forum.