Oh, dear. Poor thing.
Funny you should say he's got Crohn's. My b-i-l has it, and my nephew has something-or-other, and in fact, went in for surgery last night and didn't actually have surgery until this afternoon. He had severe hemorroids and while he was under, decided to do a colonoscopy.
He's on a mostly gluten free diet (what teen doesn't cheat?) and he gets sick fairly often. He's had pneumonia twice in the last 20 mo's, and went to the ER once for it.
That is all to say, that things can masquerade as other things and I'd be doing a workup, for sure.
Please let us know what the dr says about the test results, and how your son is doing.