As for the Reactor, maybe it could emit a radiation that damages aliens when they get near, with an increasing damage rate the longer you remain close.
So for a short period, an alien standing near the reactor would recieve no damage, and then damage would increase depending on alien size, and distance to the reactor. This way, low classes would be prevented from standing on the reactor, and the larger classes would be less inclined to screw around when within the human base.
Not a lot of damage mind you. A large class that charges in, takes some structures out and gets gone should take only a few (less than ten) points of damage. And that's only if they spend a large amount of time near the reactor.