I agree with you, although I think most "good ideas" are just happy mistakes, especially when it comes to mods. Other than the game being a massive disappointment, it's still possible someone may accidentally create the next "good idea". But in the history of video games, how many mods spawned a billion dollar franchise or genre. I can only think of 2, Half-Life and Counter-strike (outside of CS, essentially invented competitive gaming/e-sports), and War3 and Dota.
I'm more familiar with CS, out of all the mods and maps, I don't see any gungame, cs-surf, prison break, etc... franchises. It's rare, but it does happen. Chances are there will be no money to be made, but with the EULA the way it is, Blizz has rights to whatever may come.
As I kind of mention above, there is just no way for Blizz to even guess that DOTA would have turned into it's own billion dollar franchise. Even among extremely popular mods, there is no reason to believe that one would be worth anything outside of it's source game.
I don't know if this will stifle creativity, logically I would say maybe. But I think in this day and age of easy education, anyone that has a good idea is going to set off on their own and not use mod tools. During WAR3 prime, game creating tools and education were no where to be found, the easy to use tools of WAR3 made it a focal point for creation. The Warremade doesn't have that creative advantage.