Holy Wars are broken, mostly because there's no 'war' part involved at all. Either changing the mechanics or simply returning to the days of only the Divine being able to start/end wars seems like a good plan because right now they add nothing at all to the game. People don't even care about defending their religions and essence in terms of 'resource' is just neverending.
Essentially, war is being declared and as soon as it starts instantly surrender. All that happens is that the defenders have to spend a crapton of time raising new shrines. There's no glory. No conflict. Nothing. And it sucks.