Being on Steam limits a lot of what we're allowed to do with the game, and how we're allowed to talk to our users. We (probably?) wouldn't be able to, say, sell capes or have a map market place on minecraft.net that works with steam customers in a way that keeps Valve happy. It would effectively split the Minecraft community into two parts, where only some of the players can access all of the weird content we want to add to the game.

So, no hidden conspiracy, just not a good fit at the moment. And he even mentions that they're still talking to Valve about bringing the game over to Steam. After all, Minecraft is , so we know he must be willing to make at least some compromises.