Well there aren't going to be too many people that will help you on this subject on here. I asked the same questions for my fiance about a month ago, I got answers like the first one too.
He's already graduated basic, which limits him extrodinarily. If he goes AWOL, then he will just be court martialed and face time in the brig, bad idea. There aren't too many choices he has at this point, and it may be a long shot this late in the game, but tell him to try "consientus objecting" (sp). I'm not saying that it will work, but if that's really what he wants then he'll have to suck up the BS that they give him and stick to his guns. What that is, is a law held that after enlistment, during active duty, if the soldier feels morally he would not be able to kill someone in battle, that it's against his religion and/ or moral conviction then they will give him an "honorable" discharge. Like I said it's a long shot, but I know it HAS been done before. Also, suicidal threats are frowned upon and that is what happened with my fiance, she was released from boot and put in a seperation platoon.
To be honest, I hear that the best and quickest way out is to serve your time and honestly it will be the best thing for him, but I'm sure that's not what you're trying to hear.
If you'd like more information, look at my previous postings for more ideas, I've researched this topic extensively and again, you won't recieve much help here.
And no a general discharge means just that, "a general discharge", getting a red flag on a general, will depend on what article accompanies it. Usually what employers frown upon most are OTH's. But now a days, the only thing employers look for is how much bang for the buck can they get out of you. Of course it will require college education and won't be easy, but even an OTH can be appealed an upgraded. Ending a military isn't the end of a life, it just simply complicates things.