This might seem a little weird, but Achilles was technically a mary-sue. He was pretty much immortal, he was an amazing fighter.
When writing, if you have a Mary-sue, just keep writing. Don't care if the character seems to lack creativity. Make up that lost creativity with an amazing plot, with lots of unique flares. If you can't, kill off the Mary-sue and work from there.
One of the worst ways to kill of a Mary-sue is with another Mary-sue. If you're going to kill off a "perfect" character, don't make another "perfect" character to do the job for you. I personally would use divine intervention. If the character has powers that gods would envy, then let the gods smote the character.
Come to think of it, wouldn't gods be Mary-sues? They are immortal, they have powers that gods would envy (if the gods that are envious don't have those powers and want them really badly), and they are pretty much perfect.
I seem to go off on the first thought that enters my mind. Well, not anymore. I can't think of anything to continue off of from my last statement that still relates to Mary-sues.
Speaking of Mary-sues, I was reading this fan-fiction that was making fun of Mary-sues in general. It wasn't bashing any one Mary-sue, but the concept of Mary-sues in general.
I have to agree, though, that Mary-sues are possibly a sign of lack of creativity. It might mean that the writer is focusing more on the plot, but it probably means that the writer isn't that creative yet. Speaking of creativity, a good way of handling Mary-sues is by removing whatever makes them Mary-sues, thereby making them normal characters, and therefore are more susceptible to character development.