Something I thought may or may not work is to try experimenting with different methods of resource gathering. Most RTS games factions all use the resources the other guys use. Why does zerg need minerals? They're organic.
What if one group needs wood for all their stuff but the other faction relies on devotion to their god? The holy group will tend to turtle up naturally cause all they need is alters and their god gifts them with the needed materials. Where as the forest group needs to strike out and find more material, thus creating a naturally expansive group.
From a balance stand point since the holy guys sit around a pray all day they can't take much for damage and the forest guys chop wood all day and make for some tough face punching.