When Young head-butted Rush and knocked him out I chuckled to myself because I imagined Young thinking, "Crap, now I have to carry him back." I was stunned when Young came through alone, but I can't say I was really that surprised.
I definitely think it was in the heat of the moment. Young certainly planned confronting Rush, and probably contemplated punching him, but I doubt he had actually planned to maroon him until Rush said it wouldn't end. I don't think that was the response Young expected.
Perhaps Young's train of thought was not so different than I first suggested, except it probably went more like, "Crap, now I have to carry him back... Or maybe I don't." Young can be hot-headed, but I don't see it in him to maroon somebody on a dead planet unless they really REALLY pushed all of his buttons. I bet it took him so long to get back not because he planned it, but because it took him that long to actually walk away from Rush's body and think up the excuse for why he was injured and Rush-less.
I half-expected Young to tell Eli what happened.
I think that Eli is fully knowledgeable of what Young has done, and is at least partially complicit. Not comfortable with the situation, but complicit.
Oh, Eli knows what happened. The look Eli gave Young at the end was the look of a trusting adolescent who saw their hero come home in the middle of the night high on crack. That look said to Young, "I hate you, but you're in charge, so I'll do what you say." And I think Young understood it.
Especially if Rush does escape his exile (as we all seem to be assuming he must).
Oh, he has to escape it. He's too memorable of a character to simply fade out of the show, forgotten. And why introduce the ship if you're not going to do anything with it? There's a reason the writers put an alien ship on that planet, and it wasn't just to get Rush and Young alone. It could have easily been an alien city or other unmovable artifact. The latent writer in me says Rush must use the ship to rendezvous with the Destiny at some later point. The laws of good writing say it is so.
You know, that's one of the things I like about this show. They're not afraid to introduce something and not use it until later episodes. Things don't wrap up cleanly at the end of each show. It would make it harder for somebody to start watching in the middle, but it really rewards loyal viewers. And the fact that it's available on Hulu makes it easier for loyal viewers to stay loyal - they don't have to miss an entire episode just because they had a date on SGU night or the fire alarm in their apartment went off.
However, now that you mention it, I recall very specifically an episode of SG1 where a very low level wave transmitted through the wormhole was used to hold open the gate. I'm not sure why that couldn't be done here as well. Ah well.
When Eli's arm was used to hold open the wormhole they talked about safety features. It's possible those safety features would know the difference between a wave and organic matter and wouldn't be fooled by a low-level wave.
Also, remember that the crew of Destiny doesn't have all of the technology accessible to them that SG1 had. They probably don't have the capability to just whip up a radio wave with a frequency to their liking, or if they do have it, it probably would take them more than a few minutes to whip it up. They probably didn't realize something was wrong until 2 or 3 minutes before the deadline, since the rest of the crew was on their way back and they had no reason to think Rush and Young were not right behind them.
He isn't a team player. He is an unpopular outsider, even among the scientists. 
