Just install a bunch of cameras with motion trackers to see what's happening from the top the of the walls up. Any motion across the wall is either illicit or a bird.
The drone isn't even the issue, it's the items being delivered that are the problem. So you don't even need to stop the drone, or prevent a throw-over- you just need to have a system look to see if anything breaks the perimeter and if the intruder falls to the ground or leaves anything. If it just overflies the prison without doing anything then it's not an immediate issue (and could be halted with a directional jammer / net gun / interceptor drone). You can then identify where the payload landed and identify / collect / isolate it.
This way there's no reliance on criminals not circumventing geofencing attempts, and it covers throw-overs too. Occasionally you'll get a false positive from a seagull dropping a pizza.