Seems to me that clearances should be sent digitally from the air traffic computer to the aircraft's computer. The aircraft knows where it is, modern airliners know where they're planned to be soon, and it would know where it's cleared to be. If the two don't match then it can sound a claxon, alert the dog to bite the pilot or some such. Similarly the air traffic side will know when two objects have been cleared into the same space.
It's not trivial to do, but it's something than can be rolled out incrementally over decades and doesn't require any expensive hardware changes.