There is no doubt in my mind that, as foreshadowed by Dobermann, Carl was sent up to "the Hill" for a few weeks on juvenile charges associated with the riot, just like everybody else on the bus. If he (or Mark, Vincent Spano's character) had been charged in some way for Dobermann's murder, they wouldn't be heading off to the same juvenile detention center as the rest.
The larger answer is what was going to happen to Carl when he got back from "the Hill". Personally, I think the ending, specifically with Claude and Cory waving good bye like the young teenagers they were and with "Ohh Child" playing (rather than the originally planned "Baba O'Reilly" which would have changed the tone immensely), implies that the kids return to a very different town... a town where the parents pay attention and listen to their kids' "cries for help". As such, I suspect that Carl goes back to being a good kid, who gets good grades, goes to college, etc., etc., etc.
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