But if you're a character like Magik that's going to be actively used in a book, odds are good you're not going to be arrested and put in jail for obviously functional storytelling reasons. That's just how it is. There's no perfect middle ground there. I don't think you can tell stories where no one breaks the law, nor do I think you can tell stories where everyone serves a proper jail sentence every time they break it. That's not to say they can't do it a bit more often than they do.... but essentially this is how comics need to work. It's not necessarily fair, but ultimately that's not necessarily the most important consideration when you're making comics.
So do the Sinister Six.
Sandman went thru a slow but internally logical reformation from criminal to reserve Avenger but it was negated because John Byrne wanted him to be a villain again.
The last time Magneto tried to face turn he went to trial at the world court for his past acts.
The last time Super Heroes faced a registration act for Supers the FF fought it in court.
Now these things don't happen mainly because pretty much nobody at Marvel wants to write a story taking place in a court room unless they are forced to.
You can count the number of "Matt Murdock actually being a Lawyer" stories on the fingers of a single hand for the Bendis, Brubaker and Diggle Daredevil runs combined (tho Bru did more with stuff with Matt's Law Office than most).
In 1986, Red Hulk might have been had to do time, thwart a prison breakout by other super crooks, then help out the Avengers on some probationary basis on another adventure before getting full Avengers membership.
But Bendis and Leob don't have the patience for any of that, they wanted Red Hulk in the Avengers now.
If nobody wants to write a court room trial story and nobody aside from Bendis (and Gage) wants to write the "______ breaks out of jail yet again" story, you aren't going to get the explanations for stuff that you seem to require.
Pain shared is divided, joy shared is multiplied
All the MU is showing is a reflection of this soft on crime approach. Of cause, there are always the vigilantes like Punisher and the Mutant Racist gangs who don't depend on the legal system and just take the law into their hands. The MU is a special case, because if the law operated the same way, the super criminals would have an easy road back onto the streets, so some action is taken that doesn't quite meet the provisions of the real world. SHIELD is one of them. The Raft, Cube and ARMOR are others.
Visited NY and DC and saw Spider-Man Turn off the Dark.