It's not an all-or-nothing question, and it basically comes down to the same thing as if it was any other force in the game.
It's fine if a religion is the force behind some wars.
It's not fine if a religion gets realms totalling more than 1/3 of the continent to all act like allies.
There's gray area in between those two, in which it would depend more on the particular situation.
The general rules I hope people are taking to heart are
1) Controlling most of a continent is not a "win condition" for BattleMaster, however much it might feel so from the inside. In fact, it's almost the opposite.
2) When in doubt, put yourself—as honestly as you can—in the shoes of the people on the other side. Would a reasonable, average player find what you are doing to them fun? Do they have any opportunity to interact with it, or is it just a way to destroy them without them having a chance to react meaningfully?