It's been done, only without the "X-Men" superpowers.
Star Trek: The Next Generation had an episode entitled "Into Darkness".
Quote:
In the mid-24th century, the Angosians were involved in a protracted conflict called the Tarsian War. Being inherently non-violent, the Angosian authorities were forced to subject their soldiers to genetic engineering and chemical manipulation in order to successfully end the conflict. However, it was discovered that the process was irreversible, and when the war ended, the "super soldiers" were unable to function within or co-exist alongside the normal population of Angosian society, and as such were confined indefinitely to a penal settlement on an Angosian moon, Lunar V, and considered to be outcasts and criminals.