So? I don't see the problem with just making it one-handed and then being unable to block with it or wield anything in the other hand. It sort of makes sense because you need focus to throw something accurately. Since you can't hold anything in the other hand though, maybe you should make it two-handed instead.
Well I think it depends, are you thinking something like throwing a spear that you use as a melee weapon as well or more like you have a dedicated few weapons you can throw like knives or javelins?
In the first case I think it should be one handed. The idea to make power attacks the throw is good, though I guess you would need specific throwable weapons to use unless you want to completely remove power attacks. I also don't see why you couldn't just map the throw to a different button. (I'm assuming this is about a mod for PC)
For dedicated throwing weapons I think it would be best to have it's own throwing weapon tree.