Mods usually dont impact games in a bad way, its payware expansions that split communities, or new versions of games that are very different from their origional.
Usually, you only see mods taking over if the origional game they mod is bad, a good example is CS, normal Half-Life death match was pretty tame, and easilly bested by the likes of Q3 and UT for that kind of multiplay at that time, add a popular mod like CS to a base like this, and you'll find most people want to play the mod and not the game.
But add mods to a good base, like RO, and people will mix and match, playing both.