Becca catches Anon with her mom. If he's already fucking Becca, she tells Tina. Becca tells him to stop fucking her mom, and
Anon is cheating on every woman in the game, but no one insists on a branching system that will force him to be faithful to just one of them. Grace gets singled out because she feels bad about having sex with her sister's boyfriend. Based on no one caring about Anon sleeping with both Becca and Tina, or both Jenny and Debbie, I conclude that no one cares about the MC fucking members of the same family unless one of the women feels guilty about it. So, don't bother rewriting an entire major story line. Just make it so that Grace doesn't feel guilty! Everything would be okay if Grace didn't feel bad, right?
To me there are several points to make when it coms to that problem in general.
1. Do people care about single stories to be consistent within themselves and as such value that kind of consistency? It's clear, that a big sandbox game as SS, will never manage to be conistent across the board. But let's say somebody really likes a specific character, then he should be able to play that character's story without running into really bad writing.
As far as I see it, that's essentially DC's and Sploosh's position in this - at least as far as it's possible.
Those who really want to get every (possible) character in one playthrough will be able to do it, but they'll have to live with inconsistencies/gaps across different stories to some degree. I doubt that's ever going to change.
Yet, stories of connected characters like Eve/Grace/Odette or Mia/Helen/Yumi/Angelica ought to be consistent within themselves. And that's where Grace's troubles lie and that's part of the reason why she isn't getting more/better scenes right now.
2. Do you want charachters to have unique character traits or not?
Of course it's possible to write every character in a way, so everybody is totally fine with MC fucking every woman in town. But then you'll indeed limit the kinds of stories and characters you'll be able to use and the kind of endings you'll be able to get. If you finish the 9th main girl and you've arrived at "the same" polyamorous ending for the 9th time, it'll probably get a bit boring. You'll end up having dozens of characters, who of whom none feels jealous, guilty, etc.
Sure, it's the easy way out, but it's certainly not good for the game as a whole. At least I seriously hope that most of the main girls will have some unique trait to their stories/endings, which in a VN does of course have to include classical romance, too.
And that just leads to the problem, that there's some kind of classical romance where saying "ah it's fine, fuck whomever you want besides me" after overcoming all of these issues kinda ruins that part of that story.
I personally really liked that fact that Eve (as a trans girl) is the one who got a romance arc, opposed to let's say being a cuckquean like Roxxy or viewing MC as some kind of money making sexy toy like Jenny.
That's why proper branches are needed, as they enable better stories and more/deeper emotions, as you aren't limited by the fact, that you necessarily have to arrive at some "MC is going to fuck everybody ending" once you are finished.