I find the logic (that Jill is Bella's only friend therefore this dialog must be referring to her) lacking. Whatever happened to Bella clearly traumatized her. It's well within reason to think that she might lose friendships in that process - either as part of whatever caused the trauma, or as a result of her behavior changes afterwards.
But she explicitly says/thinks, "They aren't intimate with friends either", referring to herself and something she did with a friend. How could she be meaning that her "behaviour changes" because of the situation with James caused her to "lose friendships"? It's not even remotely close to suggesting that. She's chastising herself for a past tryst with a friend because it relates very much to what's going on with the MC.
Just follow the train of thought she's having; she spoke to Jill about her dating the MC, in doing so she seem to hope it will end what she feels for him, it reminds her of how she crossed that line with a friend, then she asks James for forgiveness. So whatever happened with this friend is related to why James is no longer around and not about her losing a friend because of her break-up.
On top of that, Bella specifically says whatever happened before was "different." Becoming carried away while making out with Jill the way you describe is almost the same as what she's going through with the MC. Unless we think Bella takes a very different view of same-sex actions, it doesn't seem like there's any difference.
What she's going through with the MC is a powerful feeling of lust and horniness whenever she's with him that takes all of her willpower to resist ripping his clothes off. With Jill, it may have been a momentary lapse in judgement/inhibition. These 2 things would not be remotely comparable and would certainly qualify as "different"; the friend incident was an accident, the MC is pure lust.
Lastly, I think you read too much into Bella staring into Jill's eyes. It's possible, but it's also possible just seeing Jill in the bed at all was the problem. In my view, Bella wasn't worried about kissing Jill in the slightest. She was uncomfortable with the reminder of whatever happened, so she turned around to get "it" out of her mind. When Jill tried to address the situation, Bella shut her down and seems to have gotten snippy about it (hence Jill's "Wow"). Jill's reaction, in turn, seems like she took offense to Bella's rebuke.
It's not just them looking at each other, it's about the wider context of that scene. They've just spent a night helping someone drown their sorrows with wine (something that the 2 of them may have done before with each other), they then spent the rest of the evening with a guy they both like and who they are both very much horny for, then they get into bed into together when they're likely feeling inebriated and horny. Plus, the way those renders are presented makes it seem as though you're looking through their eyes; first we're Jill looking at Bella, then we're Bella looking at Jill, and the next render Bella has turned away from Jill and Jill seems concerned by it.
The set up to this scene and the framing of it highly suggests an air of tension between the 2 at this moment, then when you add the fact that they're in a bed wearing lingerie, it adds a sexual component which then would seem to be compounded by the following coversation about something that won't "happen again". If this turns out to be anything but Bella and Jill sharing at least one moment of intimacy that they've since put behind them, then DPC will have written a massive red herring and managed to do a reverse Occam's Razor because I just don't see a simpler explanation than this. Any other theory I've seen just doesn't seem to make as much sense and doesn't fit with the words being said.
I got the idea, but I'm wondering why anyone would want to be in a relationship with a girl that's not interested or even able to have one. This isn't aimed at you specifically though.
But just because they won't be in a relationship with the MC of this game doesn't mean that they couldn't be in a relationship with someone else or wouldn't want to be in a relationship. That's kind of the point of these fantasy lists; if you
could be in a relationship with any of the side girls, who would it be? That's the premise upon which the lists are based.