So playing for the first time since Beta, enjoying the new starting section.
Being the good ally I am, I murdered all my future allies and looted their corpses of potions, resurect scrolls etc.
Then rushed to Fort Joy to see if I screwed my safe (since I wasn't really wanting to restart already), but nope; Ifan and Lohse where alive and well in the fort, albeit naked.
Ifan died in combat since I ignored that, but Lohse joined me, and upon joining her nakedness changed into gear, potions, scrolls and all.
So basically I got about 4 free resurrect scrolls, healing potions etc. doing this with no downsides.
While screwing you permanently out of allies is probably too harsh, this is probably a bit too beneficial with no penalties at all.