One thing you could do is dramatically lower supply in pagan territories so that invading troops lose TONS of people just to harsh conditions/lack of food. This would also make seiges of pagan lands BRUTAL because of how many troops you lose.
The other thing would be that the Pagan's shouldn't have Holy War CB's per se, but they should have some kind of Reclaim Lost Pagan Land CB instead. the pagan's weren't unified like the muslims or christians so there was no central order saying "kill all the christians/muslims" so a Holy War doesn't make sense. What does make sense is for the Pagans to try and reclaim the land that is gobbled up by Catholics so that it doesn't just become a big "land grab at your leisure" area. The Pagans would fight back...
but then again if the Pagans send their troops out of their lands, then every smart catholic surrounding them would declare war and gobble up the defenseless lands.
Let's be honest, it sucks being a Pagain in a Catholic world
Summary: Lower supply limits in pagan lands by a lot so attacking them is costly not because of enemy troops but because they have crappy lands.
edit: Looking at OP it appears his issue is that you can play as pagans but it sucks because you can't do anything. Make a new religious group "Aggressive Pagans" as a subset of of Pagans that lets you declare Holy War against non-pagans.