"Hey, why should I care that the rules of Solitaire are that you have to alternate the color of suits? You don't have the right to decide how I play my single-player game, and if I want to place cards without alternating suits I will."
Yes, sure, there's nothing stopping that example from happening, and someone doing that isn't really hurting anyone else by doing so. But it's not the same game, and if you did that and told people you were playing Solitaire you would be lying.
So, basically, to answer the question you posed in your first line, I'd say that your claim that the devs fixing the game to make people play the game the way they intended is absurd and restrictive is something that I'd find to be a ridiculous statement. I mean, the original exploit would be akin to something like finding a way to get plentiful healing items and ammo in, say, Silent Hill - it completely ruins the entire point of the game to the extent that it's not the same game, it's just a rather boring game where you kill some monsters. Similarly, essentially removing vassal management from the game by making everyone theocracies turns CK2 from a political/dynastic simulator into MSPaint with Europe as the background.
Even if multiplayer did not exist, the devs would still be completely justified in changing/nerfing/fixing things in order to make the game play more like the game they wanted to produce. Don't like it? Get some mods. That's exactly why they exist.