Young doesn't have the luxury of time nor supplies to try and keep Rush around (as in lock him up), whilst he tries to figure out Rush's endgame. The fact that Rush knows about the ship makes him even more dangerous as a prisoner, as no room in the ship is likely to contain him.
Beyond that, the bottomline is, if the commanding officer of an already shaky expedition, or one of his own fellow scientists means nothing more than an annoyance in the way of Rush's goals [whatever those may be], then Young has no reason to believe that Rush wouldn't sacrifice anyone else on the ship just as quickly, maybe except for Eli. Especially when Rush is willing to admit that he won't stop trying to do whatever he's trying to do...which he won't tell anyone.
LadyVader: What's with this, "mess with the commander" bull-crap? I take it you have never been in the military, nor in a pressure situation [like combat] such as the SGU personnel are in. I have been in both. You have NO idea how important a strong, commanding presence is in that situation. What I mean by that, by "messing with the commander," you ARE messing with the rest of the crew as well. Not to mention Rush HAS messed with everyone else in an uncountable number of ways...not just "the commander." Not the least of which is, the fact that he's the reason they're all even stranded where they are.
