Instead of banning a character, why not learn how to overcome it? If you're worried about the game stagnating, don't be; if someone only knows one strategy, they're not going to get very far in a tournament anyways. The more choices there are in the tournament, the more adaptive you have to be to win, not less adaptive.
If we're going to make video game comparisons, why not look to a more competitive genre? Such as RTSs; look at how Blizzard handles StarCraft; they're constantly tweaking things to improve balance between the races, and they've never outright removed a unit (at least, not once the game was released; they did, of course, add and remove units during the beta stages), but instead made subtle changes to each to make sure each unit is useful through the entire game- and mind you, it's still a work in progress; the original StarCraft had ten years of patches, and is often considered the shining example of competitive video games. Can you imagine how much weaker the game would have been if- instead of balancing the game- the developers simply said "well, why don't you guys just each choose a unit of your opponent's to ban" instead of working to make sure that they didn't need to ban the units?