If there was a button "Merge realms" in the game, and you were not allowed to click it, then it would be easy. Sadly there's not. What you call realm mergers are in fact series of perfectly legal actions which have an undesirable end result. Therefore it's all about intent.
I think I get what you're saying. Just disallow it mechanically in-game.
There should be some sort of check when a duke tries to defect with his duchy: If the number of cities+strongholds in the duchy is equal to the number of cities+strongholds in the realm, then he should not be allowed to switch his duchy's allegiance, because the rest of the realm has no cities or strongholds left.
