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.

Well, while it doesn't screw you over permanently, it does completely break the questlog. Each time I load I get journals updated with "X is dead" entries, making keeping track of teammate quests difficult. Even though I can still progress the quests themself forward just fine.

http://steamcommunity.com/sharedfiles/filedetails/?id=1141073629

Yes, this does break the quest log. I killed everyone on the ship, and then recruited Red, and when I escaped on the island with Red, the quest log said Red was dead while I was talking to him.

Otherwise, I don't think this is much of an exploit. The loot isn't game-changing, and the story tells you why they're all alive again.

I wouldn't say getting 5 free healing potions and resurrect scrolls that early ingame is a small potatoes.