Okay, I don’t know if you’ll ever read this comment amidst all the chaos, and forgive me—English is definitely not my first language—but please, don’t change your story.
This was the result of years of hard work and genuine effort, and it shouldn’t be handed over just to do what they want.
I’d suggest removing the scenes that could cause issues (unfairly and for no real reason) from the base game, and releasing a DLC with that content instead, so the story can continue the way you originally planned.
It wouldn’t even have to be posted on Itchio—it could be shared on Twitter (I still call it Twitter), or even through a Patreon for the extra content.
Anyway, I just don’t think you should give up the incredible story you’ve created.