Games are constantly changed when some aspect of how they are coded isn't giving the desired results. No one was breaking any rules killing HQ, but the effects of it were taking away from the game. Doesn't matter if players were right or wrong in complaining about it or logging off when they weren't having fun. You can't recode players, only the game.
There are other ways it could have been handled like having radar around HQ, changing what makes it flash, increasing the damage needed, closer resupply or defense fields on some maps, etc, etc. I'm guessing that with a new release coming out, the down time band-aid was the best choice when weighing time, resources and results.