It may have originally ended differently elsewhere but in the anime from the start I felt it was heavily telegraphed. I'm disregarding other material here. Of course everything can end differently but what I mean is that the TV show was consistent in it's tone and messageIt's relevant when you are making claims about how it couldn't have ended any other way, Obviously it could, because it originally did. It wouldn't require any out of character acts to fix that ending, accepting that situation is out of character if anything.
and so for there to be any ending but what you got in the last episode would have been jarring. Of course they could have written the entire show differently and then it would also make sense for it to end differently.
Regarding Shinkuro accepting the situation
is it really out of character? He's now surrounded by two different old ass powerful shadow families, seems pretty accepting that those two girls are going to learn to become trained killers as a matter of fact just because of the family they wore born into. To me he never really outright opposes the notion of being bound by some tradition just opposed to the idea of being enslaved by it. A reformer rather than a revolutionary.