Exact same issue and scenario here, I spoke with her after clearing the camp but before having the quest and she remains hostile.
Vathek replied to Gromnir's question in Pillars of Eternity II: Deadfire Technical Support (Spoiler Warning!)I had this same issue for 50 hours and all the way up until level 20. I actually didn't even know that random events existed in Neketaka until I read about the Griffin's blade and decided to try and get it. I actually went back to an earlier save (around 45 hours in) to complete the Family Pride quest cleanly, and went to actually meet with the Principi in Dunnage and Deadlight. I had previously completed Blow the Man Down, but had never went to Dunnage to speak with anyone there or respond to the missive to go back to meet with Aeldys. On the main quest I've been at the point to go to Magran's Teeth for quite some time now and have primarily been clearing out all of the bounties, map completion and side quests. I don't know if this is working as intended or not, since the criteria for these random encounters doesn't appear to be documented, but this was my experience with it. It seems like you're expected to at least meet with all of the faction leaders and open up their quest lines before these events show up, even if you don't want to be a pirate . Otherwise there may be some other aspect of the situation that I've not accounted for...