I agree entirely with OP. Once the barracks/WF/PP is destroyed the game gets really boring (depending on the map and whether you like to play infantry or vehicles), and once the refinery is destroyed the game is over—there's no point in playing any more.
Here are two potential ways to change this:
#1) Easy Fix: Increase the HP of the refinery and have buildings take less damage from the Master Control Terminal (engi rush is really too strong, especially in pub matches with smaller numbers of players). Also increase the global trickle of credits and make it continue even when the refinery is destroyed (losing harvester income is already a massive disadvantage). A surrender vote option would be nice as well, rather than having people leave and just sitting around waiting for the game to end.
#2) Thorough Fix: Make it so that once a building is destroyed, it counts as destroyed as far as the base destruction victory condition goes, but make it so that it the functionality of the building is restored after 5-10 mins; also make it so that the restored/damaged building has only half of its normal max HP, making it easier to destroy subsequent times. This way destroying buildings still gives a significant advantage, but it isn't a game-ender, nor does it make games boring by removing the aspect of the game that people like (either infantry or vehicles, or both). If people are worried about logic and realism, this breach of realism actually already exists, since the war factory/airstrip will still make harvesters even after it's been destroyed.