1. Once he saw he was outnumbered, he was in "buying time mode"... waiting for an opportunity. And once again, decoy... He was good enough to defend himself against bullets even while he was in his "normal mode", so your "captain who gets killed without resistance" is misplaced. At no point was it mentioned he was cool though, I simply think your hate for this particular character seems quite overboard for reasons I can't fathom, particularly compared with the abundance of shitty MCs out there. So that you have this strong reaction for this one is mind-boggling.
Anyways, this is such a common circumstance in whatever medium in which a character enters a room full of more baddies than expected that's it's not worth the nitpicking here about his behavior. I'm pretty sure Van the Stampede would've done the same... I think he did actually.
2. He didn't revert back because of mental issues, an external source (Ikaruga) used it to bring him back to his senses, to ground him. This to say that it wasn't because of an intrinsic weakness that he didn't go through with it, but someone from his team brought him back before he could go berserk. For some reason that would've been bad, and that's not ON the main character, that's ON the circumstances that would prevent the main character going berserk being a positive thing. We don't know what those are yet.
In fact you might say that the flaw in him is the one that makes him lose control, not what reverted him.
3. I'm honestly questioning the premise of "eradication of magicians", at least from the purview of the students. We got Kusanagi seeming to scold the sniper for head shots, we have Ikaruga stopping him from killing the mobsters, we once again have Kusanagi stopping Ootori from killing the murderers at the end, explicitly stating that she would lose her inquisitor status. So this brings us back to #2 on why Kusanagi didn't go through with the massacre as it was.
4. It's not useless to mention that they're students, it's important to understand that they aren't perfect soldiers and will be prone to mistakes, that everything wouldn't and shouldn't go all smoothly.
Anyways, I'm not trying to make sell you on him being a good character (I'm of the opinion that there hasn't been anything noteworthy one way or another), but that I think your dislike to the exponent you've brought to this discussion seems highly misplaced... particularly when the series is trying, and to my opinion unsuccessfully, to mix some humor and lightheartedness to the serious aspects of it.