I've noticed that although the Strawhats do a very good job of decommissioning the villianous leaders, they tend to not stick around and make things stable afterwards.
In a few cases, there was just a single man or small group who were causing trouble, and society would heal itself if left alone (Skypeia, Syrup Village), but when there was real mop-up work required (Alabasta, Arlong Park, arguably even Enies Lobby), they tend to dash and leave it to the Marine or local authorities to finish getting rid of the residue of the problem.
Now, this gets interesting in Thriller Bark. As I see it, there's going to be a lot of cleanup required. Just to figure out an ethically valid way to dispose of any remaining zombies and loose shadows is going to be a mess. Arguably, it's a problem beyond their technical ability too. Only Chopper has an outside chance of fixing it IMO, assuming Hogback doesn't turn sides at the end.
They can't ignore it. A huge ship full of zombies and ghosts adrift will be a risk for others.
They can't pawn it off on anyone else. There's nobody who knows it's there.
So how are they going to return Thriller Bark to normalcy when it doesn't seem to be something they have experience doing?