First of all, mutants are fucking dangerous. Not necessarily inherently, no. I mean, if there are mutants whose powers are simply to explode at random or something uncontrollable where they wiped out lots of people, I've never heard of it. But most of them can wreak an enormous amount of havok that is simply beyond the average person, or even the average natural disaster. It would only make sense to register them so you know what each is capable of, much like people have to have their guns registered and the like. It only seems like a prudent thing to do and the bare minimum of what is necessary. I mean, look at it, nightcrawler, with what is really a sissyboy power, by himself can penetrate all the way to the oval office. God only knows what cyclops could do from a book depository if he got it into his head to blast some shit.
Mutants should also definitely get the death penalty, or just don't even bother to capture them alive if they go rogue. The countermeasures needed to keep them imprisoned just aren't worth it. Why should the tax payers have to pay extra for a completely non-metal prison cell hanging in the middle of nowhere? I figure a sharp axe or slug to the brain is much more cost effect.
There's always been that moral question about whether it would be right to kill hitler if one had found him as an infant. When the cost to society and individuals is that great, the ends definitely justify the means. In those cases they should just cap the bitch and be thankful they had the oppertunity to do so.