Making a new post as it's been about half a day.
Responding to your question now, what I would do if a marine I was hunting and actively fighting, fled to FOB and was defended by his comrades.
I would cloak and back off, waiting patiently for my prey to leave the FOB. I may or may not hunt others during this time, but I would not forget that they ran from me. I do not intend to take reckless action however, nor am I going to spend an entire round spying on one marine that fled from me to FOB. I won't put myself at high risk for one marine, nor will I attack anyone inside or around the FOB where avoidable as I don't want to affect the round in a significant way.