What about those films where for the original release the studio didn't want to get a 'G' or some other rating, so they throw in a few things to bump it up to something more reassuringly 'grown up'.
I've seen more than a few films where the violence or nudity or vulgarity is just really tacked on. I wouldn't necessarily say that the higher rated version automatically always represents a truer version of the director's intent.
Typically in these cases the Directors are forced to add in the bits, or have some input since it's a studio mandate. When they don't it's a case of the film being taken away. Look at "Scott PIlgrim Versus the World". Edgar Wright was mandated a PG-13, so any vulgar language was censored on purpose so as not to get an R, which let the one instance that was allowed under the PG-13 to hit harder and be an actual moment. (going by memory on this one.)
Films should be presented with the directors intent intact. What this "Clean Version" thing is, is someone deciding what is potentially offensive or not, with little regard to the directors/creators intent or vision and snipping it out.
I'm of the opinion that if people don't think a film is suitable for their kids, or themselves, they should be able to garner that knowledge off the posters for the most part and wait until the kid if old enough to watch the film or make their own choice.There are way too many movies out their to watch all of them, it's okay to have your kids miss a few that may be objectionable while having plenty of others for them to watch in it's place.