Yeah, they probably could have wired up some sort of fancy multiphased shield, or rapid frequency shifting, or a phase-masking system, in some way that would be impractical to put on a capship but might work on a planet. McAuliffe was designed without consideration to defense against shield-penetrating torpedos, so it's probably not a perfect example of what could be done by the time of Fleet Action to defend planetary targets against them. I agree it's probably pretty unlikely, though.
Incidentally, would planetary bombardments generally use phase-matching torpedos? They used them at McAuliffe, but they had to send torpedo bombers down to deliver them. In Fleet Action, they were just raining a whole lot of nukes from orbit. Since you need to do the phase-matching step, and that takes time, I'm not sure if city shields make complete sense to begin with (maybe they had them, but took them down after the McAuliffe debacle). Point defenses really make the most sense, from everything we know.
Perhaps the most insight can come from Blair's penetration of the air defenses over Washington towards the close of WC4. Tolwyn's friends were expecting him, and the Confed defenses did seem activated against his approach, but he didn't seem to have to put up with more than a few fighters, and the cloak got him the rest of the way down. That would also seem to argue against a shield, although maybe it would interfere with normal traffic too much, even if Tolwyn made some mutterings about a possible terrorist strike or something by those big bad Border Worlders.