I'm not sure why you put Sayaka down, as quite obviously she's going to wind up dating both Kyoko and Hitomi.
On a more serious note, I'm not even sure if we could ever talk to Kyoko about her crush on Mami. The best we can probably do is tell her to talk to someone else. Maybe Masami and Hiroko? They know Mami, they know some things about accepting one's self as a lesbian, and Kyoko will probably be more inclined to listen to another student of Mami - a peer.
Why do you think she made a point of coming along to talk to Kazumi in the first place? Honestly, she would've been my go-to on this subject too for all the reasons you addressed above.
What I think Sabrina can personally offer Kyoko is acceptance, and our adamant refusal to let her insult our friend Kyoko, who despite our differences and misunderstandings, we care about a lot.
My main worry regarding the Witchbomb with Kyoko is that it'll reinforce the idea that she sold her soul to the devil and will be facing an eternity in hell for her sins. And that she'll conclude this is
correct, that it is what she
deserves. And that
can not be on. Both because
no one deserves this, and because
Kyoko is a
good person. So even if we accepted this was okay for a bad person to suffer like
this (which we
do not), Kyoko is
not a bad person, so she doubly does not deserve that fate.
We may not be able to get at the root of her feelings about Mami, due to how much our presence is complicating things, but we might have better luck chipping away at the moral and philosophical foundations of her self-loathing.
Kyoko's smart, and her self-justifications are deeply rooted, but I for one, feel much more confident getting into the weeds with her and debating the morality of hell than I ever did, for example, trying to unravel the cultural beliefs that make the lichbomb so uniquely traumatic to our friends that I only know are even a thing thanks to my interaction with this fandom.
It might also be worth trying to track down some of the former members of Pastor Sakura's congregation. Learn what exactly it was that he was preaching that lost him his flock in the first place and maybe get a sense for how things changed when he unknowingly got mind control powers. Plus, maybe see if any of them are still under his influence.
We did recently work out that Feathers is likely a consequence of an out of control Wish running around doing things on her own. If Kyoko's wish is still having active effects on people, tracking those people down and working out how to free them from those effects would double as a redemption arc for the sake of Kyoko gaining some peace and as a trial run for how we're going to get Feathers to play ball with our agenda to break harmful systems and save people.