I think the new Saints Row game had the best solution, they allow cheating but you cant get achievements or anything like that, and it disables auto save while you're playing. So basically, you can play coop with your friends and enable cheats to screw around, or you can play the game as intended.
Valve sort of does something similar with their allowance of non-vac servers that let server admins load up any mods, any rules, and any server settings they want, but again you dont get certain things that make more "competitive" games fun for more players.
I absolutely agree that BF3 and MW3 should ban players who blatantly load up 3rd party programs and use those to exploit the game in an open server where everyone else is just trying to play. That should not be allowed, but they SHOULD allow people to run their own servers, with what ever settings they want, and just keep those servers in a separate list.
Exploits and stat "boosting" I don't really think deserve a ban though, I think a stat wipe would be the smarter move, or again like Valve did with TF2 when it caught people idling for items...they removed many of their items, and rewarded non-idlers with a free halo to wear.
COD series is a global marketing platform, it really isn't a game in my eyes. They are more concerned with putting a COD label on a bottle of Mountain Dew, a MW3 stick on a headset or mouse, or all kinds of gimmicky advertising ventures that go so far as to have Chrysler build them a Jeep Wrangler. That is not gaming...that is just selling useless shit on the back of what used to be a fun franchise. So frankly COD franchise has lost my support thanks to the pile of crap that is MW3, and they won't get my money again, certainly not Infinity Ward since they are the worst offender.
Frankly I think the only reason MW3 is even banning anyone is cause they know people will just go buy more keys or new copies of the game and thus giving them more money. I don't think it has anything to do with protecting the enjoyment of fans anymore. Perhaps I am just too jaded...