Need more details on how this could have happened, you're post is very unclear, what happened, how, when, what npcs are around still. Off the top of my head I would say scourge 1st of all then make one of his lackeys take his place. Not sure I would have let it happen though myself. One thing I don't understand is where did they get the poison to do that kind of damage, there is nothing on the ship I am aware of that will kill an npc even with a bad fort save? Sandra is around, she would have made to cure him or failing that the ships surgeon.
Not sure how you don't get Harrigan involved and needing to punish the PCs, unless he is charmed by thier unmitigated gaul, or feels he needs the extra hands when the new ship pulls in.
OK kind of makes sense now ta, not sure I would have allowed the posion situation though, 1 dose of pioson only coats 1 weapon not multiple Shurikens I think? Poison is expensive and its a one shot once applied thats it for that dose.
Regardless however, its your'e game you play how you want.
As for what to do.
1) Promote Scourge to Pluggs place and use Plugss stats maybe to make it easier.
2)Promote one of the lackeys Jape or Slippery maybe or even use Cogward instead, into Scourges old spot use Scourges stats mabye instead.You could have 2 subordinates to Scourge to watch his back, make both CR3 maybe
BUT
DON'T let the PC's get away without punishment. They were warned on Day 1 what would happen if thier was a murder, you menetioned that some NPC's spotted them and they didn't care again they have been warned.
My advice here..Harrigan gets involved. This guy is going to be pissed big time. Have one of the NPC's propably one of the lackeys like Jape report to Harrigan they saw a murder, back it up with the other NPC's. He calls a rollcall on deck the next day and pulls the PC's out, use his higher officers if needs be like Riaris to make sure this happens. Then have a Jury of sorts all the while having Scourge and his lackeys gloating. They will need to do some MAJOR role-playing here to get out of a Keelhauling I think. At the very least they should get the Cat, tied up on the post so they go down to neg HP, healed to maybe 1hp then chucked in the sweatbox for 2-3 days.
Whatever happens they need to be punished BIG time.
And remember, Harrigan is a ruthless enigma and untouchable, if they thought Plugg was mean, they are in for a world of hurt.
I think they have just made things VERY difficult for themselves for now at least.
Im liking the fact he's not dead. That opens a whole new world of possibilies, not sure how you could do it but how about have him appear on the Man's Promise when the players are on the isle of Bones, there are a couple of days where the PC's are off the ship. He could come on board and hijack the ship and plan the ambush as written.
Regardless problem solved, Plugg not dead, he comes back for revenge in some way that you see fit. PC's still punished as no-one is aware he's alive.
Win, win.
Let dead Pluggs lie. The PCs got rid of a nastie. As Ferrin suggested replace him. In the morning report a number of lost crew due to the storm. Because they are short handed the PCs escape death, instead they get the box and a good whipping. Run the remainder as written, perhaps with your side quest with the PCs treated as trap bait not as trusted treasure hunters. When the attack on the Man's Promise appears. Pull the PC's out and have the given the instruction as listed. Durring the fight the PCs have an option to warn Harrigan if so the drunk and happy treasure rich Harrigan forgets the murder, angering Scourge to no end and convincing him to not take the ship back as Harrigan planned but strike out on his own in place of Plugg. If the PC's don't warn Harrigan have Harrigan give orders to Scourge to kill the PC's once things on the ship are set right. At this point run it as planned. Though with your group I warn you they might mutiny before the planned mutiny in the adventure.
or go the other route and have Plugg come back for revenge later date further on in the AP.