It was from if I remember correctly, her thinking about her guilt of it and him being his friend or whatever excuse it was that she decided to to get in a formal relationship ( inner dialogue wise ).
However this part you said " Jeremy, on the other hand, is involved in both friend groups, and Eva would have to juggle a lot of storylines and character interactions going forward "
I could see that being the case however ( you mentioned down later about Lena being hypocritical which is true ) Holly technically is also intertwined in both groups to some extent and hangs out and interacts more with Ian on a possible daily base vs Jeremy as Holly does hang out a lot with both Lena and Ian. However in game wise, if Ian went on a trip with Holly and smashed her and they talk about it she get's angry and refuses to actually commit and berate him... but if they are actually in a relationship and Ian does nothing to Holly and Lena is however doing things on the side with Holly, everything is fine and dandy, my point with that is, that it can be skirted the same way it is skirted with dialogues when for example Ian asks Holly how it is going with her and Lena's friendship and if they have good times hanging out. Holly dodges it like a champ.
So I think that given that Jeremy and Ian in comparison the interactions are a lot lower and so when they do hangout all they would have to do is pretty much barely or not interact with one another during times when they are all around and it should be fine.
But yeah still not happy at the fact as Ian you smashing Holly is no go for relationship but Lena can get all up in there and be in a relationship just fine.... that is bs.