Well, you can certainly go on and finish the game without blowing up the ship or forming the alliance. In some games, I skipped this part (did quests for both sides up to that point), and there was no difference at the end.
However, far as I know, unless you do the alliance, the two will stay in your party kinda forever. Not sure if even death (theirs
) will help you get rid of them.
My suggestion: follow through on the alliance. Remember to see Yamir again afterwards, so the two will leave the group.
Nightowl2