In the last match I played, a player from the opposing team rocket jumped onto my team's refinery and planted the nuclear strike beacon (map was Red Zone, if that matters). Because no class that has a disarm function has any means of rocket jumping, I think this tactic is someone unbalanced, since the beacon is essentially impossible to disarm unless a defender goes back to the spawn room and gets and mass driver and figures out the best way to get up onto the building, which may still have a defender on it waiting to kill him anyway. Rocket jumping onto buildings to plant beacons basically feels unbalanced to me because it puts a big advantage to the attacking player (and there need be only one, rather than a team) both in defending the beacon from people disarming it and also in terms of the time it takes for people to go and get mass drivers, especially if they don't immediately realize that the beacon is on the roof of one of their buildings.

I think that buildings should have invisible walls above them so people cannot get on top of them.

All buildings do have invisible walls. This used to be a trend years ago with jumpjets flying on the (then Power Plant) Research Center's roof and planting beacons, which also instakilled buildings externally as well.

I noticed the Ref window's ledge was able to be walked on, but I didn't think people would actually plant beacons there.

This is a little worrying.

I have tried this a few times and it's damn hard to actually plant that beacon at that height with an awake opposing team. So hard that I don't think it should be removed. Rather be seen as an intuitive and creative play.

The ref is also vulnerable in this way on the ice map with tiberium in back tunnel if someone want's to do anything about it.

I don't think planting beacons on places that are inaccessible to disarm classes (that don't have any additional weapons) is intentional.

It isn't. I've prevented it on a few maps. Which map is it?

I don't know names. :V

It's AOW18 and fixed.