Stealing the concept of "Prayer power" from the Black and White series, I think that the zeal stored inside of a clan's religious altar should greatly reduce the damage that a God does to the altar and the surrounding structures in a fairly large radius. The zeal is consumed until depleted, then the structures take full damage again because the faith is considered abandoned.
Gods should also be down-right incapable of damaging structures under their own protection.
(Clan cannot use a Set altar to attack another clan who's city is under the protection of Set for example.) ((If this is too restricting with the 6-8 Gods we're supposed to end up with, maybe a stronger version of the damage reduction instead of damage immunity.))
This would give defenders time to try to kill the enemy temple, take out the avatar, etc. Something of a count-down clock. Once live human sacrifice and prisons are implemented, this also means that people could pour sacrifices into an altar to attempt to weather the assault.
Please note, I did say reduced damage. Sandstone under the protection of Yog is still sandstone. It is still going to crumble after two avatar hits or something relatively low.