"Is there really going to be a problem with a UAV operating at 50,000ft? "
...At 50,000' I agree there's not likely to be a problem. At 5,000' or 500' (and anywhere in between) then yes!
Another "interoperability" issue that's likely to arise is that there's a move for autonomous UAV operations, i.e. the drone operates without somebody on the ground directing/controlling it. If that takes off (pun intended) then there won't be a pilot on the ground looking at any optical images (or physically watching) to see if the aircraft is about to hit something else.