No, the reason why she brought Lilly up was because she felt Lilly was treating her the same way Hisao was...as a broken child who had to be looked after. This was partially set off by Hisao's comments earlier in that scene about how he and Lilly had been worrying about her.I've been thinking about the bad ending more and what was said in it, specifically why Lilly was included in her rant.
Did anyone else get the feeling that Hanako was resentful of Lilly being able to be her friend *because* she was blind, thereby getting a free pass without having to deal with Hanako's looks?
First of all, I don't believe Hanako truly resents Lilly. When Hisao speaks to her in another scene where she's not suffering from depression, Hanako says she loves Lilly very much. Lilly's mothering nature secretly annoys Hanako sometimes (and not just Hanako), but most of the time she's happy to be with Lilly and spend time with her. Nevertheless, the feeling of inequity is probably the one hidden blight in their otherwise very close friendship.
Part of the issue here is Hanako's low self-esteem. In her good end, she admits she feels she's a useless person and finds it impossible to believe someone could be her friend for reasons other than pity, so it's no surprise she thinks Lilly feels this way too. This contrasts sharply with Lilly's words to Hanako when she's about to leave Yamaku in her own route where she states she befriended Hanako because she felt the latter was a kind and beautiful person, not because she felt pity for her. So Hanako's feelings towards the reason Lilly befriended her are false.
That's not to say they're not somewhat understandable. While Lilly's personality often comes across as perfect, her motherly nature is in a subtle way a glaring flaw. Mothering people seems to be Lilly's way of showing affection towards people, but in practice it tends to push them away. During the first time you meet Akira in the Shanghai, Lilly openly worries about how Akira's doing on her own and Akira is visibly annoyed by it. Likewise, in Lilly's route, Hisao eventually feels Lilly is looking after him in a way and he doesn't like it either. That doesn't prevent them from being close to Lilly, but it does make it harder for them to have a truly equal relationship with her. Lilly only seems to be partially aware of this.
So Hanako's frustration with Lilly stems forth from her own lack of self-confidence and Lilly's subtly flawed way of acting towards people she cares about.