Probably the simplest solution would be to create 2 new unique characters ( say Claires_Pirate_01 and Claires_smuggler_01 ) using the same models etc for Claires crew, -- might have to copy some dialog files etc -- this would then remove the conflicts between the side quest and the main story.
You could probably get away with solely copying their character init files, changing their ID and using the different ID in the sidequest.
I reckon there's no dialog file adjustments needed. Might be a pretty simple fix in that case.
So apart from changing the entries in Claire Larrouse quest in the quests_reaction.c file could you tell me which files I need to change to create the new characters - - and I will give it a try and see what happens.
:nk