One problem I have with Avengers Undercover is this idea that the kids won't receive any benefit of the doubt for their actions, because they're considered damaged goods. That they were considered unstable after Murderworld, and now they straight up murdered Arcade, and that's it, they don't get to be good guys or make any excuses for their actions.
The problem with this, as he so often is in such matters, is Wolverine. The kids were put through Hell, and when given the opportunity to face their tormentor (who had in no way repented or attempted to make amends for his past actions) they killed him. How is this different from the relationship between Weapon X and Wolverine? They experimented and tortured him, and now he kills people connected to the project whenever he gets the chance, and has done so for quite some time.This isn't taking into account his typical slaughterings of the Hand, the Yakuza, random biker gangs or hate groups, etc., etc.
That Wolverine's done these things isn't the problem. It's that he's done them, and continues to do them, and it doesn't seem to hurt his standing with the rest of the costumed hero set at all that's the issue. If Wolverine can kill people for no greater offense than they stand between him and the guy he really wants to kill, and he can still be headmaster of a school, serve on 3 different X-teams, and be an Avengers, why can't Hazmat, Cammi, and the rest be cut a little slack for cutting Arcade? I'm not saying sign them up for the Avengers - frankly, you could hardly blame any of them if they never wanted to do the hero bit ever again - but they shouldn't be in a situation where they're being thrown into SHIELD lock-up and treated like super-villains.
I think sometimes the worst thing that happened in the Marvel Universe was Wolverine became popular. Say what you will about whether the Punisher fits in the Marvel Universe, at least he's still generally regarded with wariness or outright distrust by the heroes (his odd team-up with Dr. Strange in Original Sin aside). I don't know if Wolverine's reputation was ever that bad, but in the day, Spider-Man and Daredevil fought him as often as they worked with him, and Captain America told Logan the Avengers would never have him. Even the X-Men weren't quite sure of him. Most of the time he was a trusted friend and ally, but every so often, he'd lose his temper, lash out at them with his claws, storm off on his own, disregard somebody's orders. Even they couldn't entirely drop their guards around him. He was a bit of a wild card, because he wasn't as merciful as the other costumed do-gooders. If it had been him on top of the bridge watching Gwen Stacy be knocked off, the Spider-writers in the '90s would have had a heck of a time explaining how Norman Osborn engineered the Clone Saga when he'd been hacked into little bits.
Which might have been a blessing for all of us, as it would have spared us the next 15 years of attempts to make Norman more like the Kingpin or Lex Luthor, but I digress.
The key was despite Logan's penchant for bloody revenge, he still had enough kinder, more noble moments you could understand how the X-Men stuck by him, even if the rest of the heroes kept their distance. He was capable of warmth, bravery, sacrifice, compassion, all those good qualities. He didn't always default to them, but they were there.
The problem is, while those qualities haven't vanished over time, neither has all the killing. If anything, it's getting worse, as he grew overexposed and writers couldn't think of any better stories than to have Wolverine slice up 50 bad guys. No, 100 bad guys. No, 200 bad guys. And the bad guys all have laser chainsaws! Ahem. Until you get to Millar who has Logan setting out to kill everyone in HYDRA, which is apparently over 40,000 people. I don't know if he managed it or not (given HYDRA's continued existence, I'm guessing not), but that's ridiculous. Yet Logan only seems to grow more accepted. He and Spidey have breakfast at Strange's Sanctum Sanctorum. He and Ben Grimm share brews and play cards. Everyone seems to have simply decided that's who Logan is and they'll just ignore that massive pile of bodies behind him. Which makes it kind of strange when they get bent out of shape about some teen heroes killing one guy, or they treat Deadpool like garbage because he kills people for money (but also saves the world sometimes), even though Wade has a legitimate mental illness.
I don't know what the solution is. Wolverine could stop killing people, or at least kill people much less frequently. Him being dead ought to help in that regard, at least until he comes back. Though I wouldn't put it past Logan to continue to kill people after he's dead. Or, go the other way, let him keep killing people, but make this an actual sticking point, where the Avengers aren't so happy to have him around, and making him headmaster of a school is not a good idea. All that ninja-killing has to be cutting into his time and availability to handle the administrative duties of the position in a timely fashion. Let him be a part-time history teacher, or something. Professor Howlett's Tour of Deaths of the 20th Century. The problem there is trying to explain the sudden about-face everyone would have to experience to put Logan back on the "not approved" list.