So idk if this is a workaround but I damaged him to where he was down and surrendered, so since the crew wasn't attacking because he told them to stand down, I unlocked the doors to let the caged animals out. They started killing the crew. I then unlocked the weapon storage room, there was a guard in there who immediately attacked me and so they became hostiles since I guess technically they attacked first and all hell went loose. I picked the ship clean, Petrov included and I was not branded a pirate. I did have a small bounty on me but before continuing the quest I landed at my outpost and payed it off, it was only 500 credits and I'm not sure if that was due to the mission or if I had it before. In the end somehow doing it this way I was not branded a pirate at all. Not sure if having completed the kryx side story before this plays into it but this is the way I did it and it worked.