Honestly, I think one way to fix this would be to give us greater control over assimilation. You should be able to confine religious and cultural conversion to a single province or a series of provinces, like in EUIV. The goal shouldn't be to blanket convert everyone, it should be to maximum their happiness so you aren't being robbed of potential manpower and taxes.
This is what I was thinking too.
Two potential ways:
1) On culture screen, decide for each culture whether you want to not convert, naturally convert, or forcefully convert.
2) On province screen, (separate from governor policy), decide whether you want that governor to leave culture alone, assimilate elites, or assimilate all.
My only concern is whether leaders in this era even thought like that. It seems like they literally didn't care unless you caused revolts.