I don't see how it will control modders, they can still use nexus if the rules are too heavy-handed. Valve has a good track record on this though, so I think it will be handled well. If not, there is always an escape clause

I just don't like it, when companies control too much.

If you look at the announcement on the Nexus, you can see their concern, that the Nexus will become affiliated with many pirates, because they can't get the Mods over Steam Works. And now call me paranoid (I can't blame you, I am paranoid regarding this ^^), but I think this might be a way to get the Nexus site down for good, by accusing it of promoting piracy and getting full control over the modding community.
@Dovakhan
Just like I said. It is a good way for people who haven't used mods before, but otherwise I don't see a point in getting Valve involved in the modding community. Bad enough, that we need Steam to play the game.