Actually, as far as I'm aware the only person being taken out of the equation here is Notch, and according to him he let someone else take charge a long time ago and has been increasingly hands-off with Minecraft ever since.
So, I doubt he was single-handedly blocking Nintendo ports. It seems likely that several of the high-ups at Mojang must have agreed not to waste their time with Wii, Wii U, or 3DS iterations. Even if Microsoft wasn't part of the picture, I'm not sure Notch being taken out of the equation would increase the likelihood of Nintendo ports.