Well, IMHO if someone manages to land or jump from a heli on top of building, avoid getting hit and plant a nuke on a very difficult to get place, he should be rewarded for it.
The real problem here is that you can place beacons in places which are impossible to defuse like inside of other structures. And a good solutions to that have already been mentioned.
1. Make certain areas, like chimneys or edges on the roof of WF slippery so you will fall down when you stand on them.
2. Place beacons exactly where you're standing not in front of players.
3. Fix collision detection of building so you can't get inside the geometry.
And that's it. We will still see beacons dropped in places that are difficult to disarm, but will eliminate ones that are impossible to disarm.