I’m doing the crimson fleet mission line. I read that if I kill people on 2 missions UC guards will throw me in jail and that UC ship won’t talk to me anymore.

If that happens can I still finish the quest line, but I just don’t have to mess with the UC people anymore? I’ve been putting this mission off because I ain’t no snitch, and I’d rather not deal with them if I can. If I stop dealing with UC will I get all the achievements?