I think I have managed to do this 2x(not 100% sure this is what caused the server crashes). After clicking send to annihilate, then I tried to move my orbital units off of the asteroid and send the engineers through a teleporter. This is to save my units from dying and using the least amount of time to complete the action of terminating an opponent's planet. Needless to say, it is a bummer to almost win. There were several people still on different planets.
I have had the same thing happen on 2 different occasions, I just didn't put 2 and 2 together until you mentioned the cause.
It happened to me too, I never really could pin point the problem. Also, we don't get the lost connection to server note anymore, the game is just frozen... I think you are right, I think "almost" everytime I start moving a planet and move satellites off, it crashes.