From what I heard on the iMore Podcast yesterday. The licensing etc is different for the Apple TV version of You Tube, so it will be staying.
If and when You Tube gets removed from Apple TV, they will obviously need to be something put in its place to allow continued access to You Tube. I think the easiest alternative to allow access to You Tube through Apple TV, would be to include a Safari browser on it (through a software update). This would then allow continued access to You Tube through Apple TV.