I've seen a number of battles where the defenders have lost the station due to this issue. Instead of using the station for cover to pick off flankers, they wait for the station to die and then get swarmed by the remaining attackers.
I would suggest one of the following options:
1) Don't deploy the ships that aren't going to contribute (leaving more battle points for the player, who can prevent flanking)
or
2) Have them wait at waypoints to either side of the station instead of behind the station, so that they form a wide line across the battlefield and prevent the station from getting surrounded.
Not letting the station get surrounded is a big deal, because that allows it to vent flux on the modules that aren't facing the enemy.