I guess I'm the lone reader (so far, at least) that really feels Lilly and Hisao fixing things and figuring it out and getting back together isn't OMGEBUL. I mean, I understand it'll be tough on Hanako to get "backstabbed," an it'll also be tough on Emi when she may have finally found someone she can try to open up to (remember, in the VN, she was very good at shutting Hisao out until she decided she didn't want to anymore, and I think she's closer to letting him in in this story than she was for most of their time dating in the VN) but in the end what Hisao does has to be what's right for Hisao. And what's right for Hisao isn't a Hanako who would still rather abandon her trip on the off chance of getting him, which sounds a lot like an excuse to remain as reclusive as possible no matter what she thinks will happen with Hisao while she's away, and it's not really an Emi who cant even cope with her own problems at this point. Now, if Emi could find it in herself to tell Hisao about the accident I'd say she's his best bet overall, but currently the only one who even kind of has the capabilities of dealing with their own problems and Hisao's is Lilly. This is only reinforced by the fact that Lilly made a choice to go back to Yamaku, thus taking control of her life, albeit belatedly, and dealing with what was her major issue, at least a little bit. There's also no rule that says a couple that broke up getting back together must fail again, especially not when at least one of them has dealt with the problems that caused the breakup in the first place.
I guess the tldr version is: Lilly and Hisao getting back together isn't bad, neither Hanako or Emi can in their current state of mind deal with the pressures and problems of being in a relationship, no guarantee of failure if he gets back together with Lilly.