I agree that logically you should get to play as whoever wins the civil war, but in gameplay terms it would almost completely neuter the mechanic. Sure dealing with a civil war would still be annoying but if you literally can't lose there is less incentive to try and avoid it or fight it out properly if you can't.
I dunno, civil wars still suck to lose in EU4, even if you do keep playing. The costs to stability, unrest, money, Monarch points, long-term economic and diplomatic maluses, the installation of an often terrible and low legitimacy ruler, etc. are significant. You often also lose territories to separatists or opportunistic neighbors who decide to press their claims while you're weak and unable to respond effectively. Still very much in your interest to win them if you can. I could definitely see a similar system being implemented in I:R. In fact, if they made it more like EU4 AND dialed up the difficulty, that might actually incentivize avoiding them more than the game currently does, because really, right now most civil wars are pretty easy to win.
You can just load up a game and play as the other side I guess, same as if you get completely conquered by a different tag. No difference for me, you lost. Doesn't stop you from using stuff outside the game to play as someone else.
That only works if you're not playing Iron Man. I prefer Iron Man, so not an option for me most of the time, and I imagine I'm far from alone in that. Also, regime change being forced by an internal faction within your own government really isn't the same as being conquered by an outside power. When Roman civil wars resolved with one side winning, that wasn't another nation conquering Rome, and Rome didn't stop being Rome after the civil war was over.
Also, again, you're not playing a character in I:R, or even a dynasty. You're playing a nation. If another faction takes power, that isn't the end of the game in any other circumstance. In fact, your entire original dynasty can die out over the course of the game with minimal impact, and in a republic minor characters come to power and leave power all the time without issue. You can also have your leading faction assassinated, or you can completely change the social fabric of your nation in some cases through events and mechanics that allow switching your religion, primary culture, capital, and even your country name and traditions. In all of those cases, the transformation of your nation is pretty complete, and still doesn't result in a game over. So why is a civil war the exception?