If pointing out the most obvious issue presented by the franchise's very premise strikes you as "over-analysis", what wouldn't qualify as such? It isn't even a matter of subtext. Believe it or not, some people like to not have to turn off their brains to enjoy pop entertainment.Lets not over analyze it now.
I think it is over-analyzing considering the movie is meant to be a comedy, popcorn flick. When the film came out, government conspiracies were somewhat in vogue in the entertainment media. This movie spun those conventions into a comical farce with several jokes centered on the brain wiping and the fact it is utterly ridiculous.
But they do work outside the law with no accountability to anyone other than themselves. Wasn't that the base premise of your claim? For example, take Batman. He is a vigilante who regularly assaults criminals, civilians, and police alike in the Nolan films (extend it further to the comics, he regularly places children in dangerous situations). Like the MIB, he does this all in the name of the greater good.Why would I? Most superheroes don't regularly assault people's brains.Do you also have moral issues with every superhero movie ever made?