The trick is balance - if your foe gets to put a Castle Brian's worth of ordnance on the table, you trundle up with a lance of Rattlers and soften 'em up with cruise missiles before moving in to mop up.
Either that, or set a Victory Condition objective that doesn't require flattening the entire complex. Perhaps an artillery bombardment knocked open a maintenance hatch on a turret, and, to win, you need to get a team of BattleArmor infiltrators there, shifting the fight to the interior corridors.
Alternately, you could use the rules that allow non-penetrating hits to score "crew killed" results, leaving you with an intact (but gooey) installation that your own infantry could infiltrate and take over. (The Big Mac book also has rules for firewalls that allow different portions of a bunker to be separated, so a "crew killed" result only kills the people manning one section, letting the rest continue fighting, and granting the possibility that a backup crew could be moved in to restore the emplacement to functionality.