I think the situation between Ian, Lena and Jeremy will be difficult to handle for Eva no matter if the former two are in a relationship or not.
I have no problem understanding why Eva decided that Lena having sex with Jeremy is incompatible with a relationship with Ian, for the reasons BloodyMares mentioned. But it’s also true, as desmosome pointed out, that it doesn’t fully resolve the situation. I think the ideal solution isn’t to try to avoid a falling-out between Ian and Jeremy, but to find a way to write it and time it which doesn’t make the branching task impossible.
Eva can choose the simple solution—when Ian and Lena are in a relationship—to keep the blowjob and sexting as secrets from Ian. But almost every one of Lena's interactions with or relating to Jeremy have been pushing the limits for what's appropiate behaviour: Watching him having sex with Louise; then not telling her that he's cheating on her; looking at and masturbating to his nudes on Louise's phone without anyone's consent; giving him a blowjob at Ivy's place; and then sexting with him and even using the fact that they're hiding it from Louise and Ian to spice their interaction.
The fact that they're doing it behind Louise's and Ian's backs, is fundamental for the story and for us as players. It’s less important for the characters, but I think it’s fair to say that Lena too is getting some satisfaction from it. For those reasons I think that Lena—even if she makes the rational decision to end things with Jeremy—absolutely should get the option to keep lusting for him even if she's in a relationship with Ian.
There's a lot of things in the story to pick up on in that case: Lena's already got that recently acquired dick pic of Jeremy on her phone… she's not doing anything wrong by keeping it and looking at it every now and then, right? And she promised him she would send more nudes if he kept their secrets from Ian, so that's only fair to do, and besides it's not worse than what she's already sharing on Stalkfap… right? And then we have Ivy, who's also doing her part to get Lena to copy her lifestyle and get her and Jeremy together. I doubt Ivy will be affected by the fact that Lena is in a relationship. And if Ivy says it's just for fun and that Lena and Jeremy aren't doing anything wrong, there's no reason to not go along with her games, right? And in addition to that, as Ian and Jeremy are best friends, Lena and Jeremy are bound to spend even more time together if she's in a relationship with Ian. That's not exactly perfect conditions to try to forget the attraction that exists between them.
And then there's the point I originally was going to make: What if Ian wants to be in a relationship with Lena, but she rejects him, and then continues having sex with Jeremy? That will certainly be an option, and Ian will almost certainly also find out about it sooner or later. That's not as bad as if Ian was in a relationship with her, but I think it's far worse than what's been going on with Jeremy and Alison, and it really should give the player, as Ian, an option to get pissed at Jeremy.
Why is Jeremy's involvement with Lena a bigger betrayal to Ian than his involvement with Alison? Well, both of the guys have known Alison for several years without seemingly showing any interest in her. Now Alison shows interest in both from the beginning, so the situation is pretty clear for everyone involved. Jeremy also gets his chance only if Ian doesn't take his, and he's completely open about everything that happens between him and Alison.
With Lena all of that is the opposite. When she enters their life, it's from the beginning as a girl Ian is interested in. And while Alison only go with Jeremy as a backup option if Ian doesn't show interest, Lena and Jeremy can start their affair even if Ian is completely invested in his relationship to Lena. And most importantly, Lena and Jeremy hide everything from him—exactly because they know (Lena, at least) that what they're doing isn't OK.
All in all I think the affair between Lena and Jeremy is bad enough—even if she's not in a relationship with Ian—to make it necessary to plan for a falling-out between the two guys on several paths. Despite his bro code, Jeremy is terrible at setting boundaries, and he seems totally incapable of saying no to an attractive woman. With Jeremy, Lena's also proved that she easily can step over the lines of what's right or wrong.
Eva could obviously just put an end to everything between Lena and Jeremy if she's in a relationship with Ian; and if they're not in a relationship, write the story in a way that doesn't end with any falling-out between them. But that means that several of the plot threads that are already established, have to be put aside. In my view, the fundamental side of the attraction between the two, and their beginning affair, is exactly that they're gradually pushing the limits of what is acceptable, in a way that—for the logic of the story—should sooner or later go horribly wrong, for someone involved and/or affected. If Eva puts too many limitations on that part of their path, I think it would also mean that we're losing the things that have made it interesting from the beginning.