The reason Hanako's arc ended at the time it did was to avoid ending fatigue. The main conflict was over...drawn-out epilogue scenes would have made the story fade away instead of ending with a landmark moment. Yes, everybody would have loved to see some d'awwwworthy scenes of happy Hanako afterwards, but that's what imagination is for.
As other people said, Hanako's story takes place over a short period of time...before Lilly even got back from her trip to Scotland. Seeing that she was still her old self around the time Lilly got back from her first trip, I'd say Hanako made more progress in her own route at that point than in Lilly's route.
It's not so much the fact Hanako needs a friend more or a lover more. Because of her deep-seated beliefs she's useless and a burden to others, she needs people in her life who aren't afraid to rely on her...people who allow her to make herself useful and make herself feel appreciated through her own efforts. Whether those people are lovers or friends doesn't matter as long as they're there for her and allow her to be there for them.
Ultimately, in the long term, I believe Hanako's better off in her own route. Not so much because she got a boyfriend out of it, but because she got to adress some of her deeper issues and demons that I believe remained dormant in Lilly's route. In Lilly's route, Hanako makes new friends, but it's still only casual contact...impressive, especially for her, but not anything beyond what she achieved with Lilly. (other than the fact Naomi and Natsume aren't blind) In her own route, Hanako shares things that she never even shared with Lilly, so I think her development, while more painful, is also more profound.
I was particularly unhappy and... well... shocked(?) at where Hanako's path went. I mean, she takes her clothes off as a meaningful, symbolic gesture of the revelation of all her physical scars, and Hisao, King of Boners that he is, thinks "OOOH SEX."
If it was merely a meaningful symbolic gesture meant to show off her scars, she'd have kept her bra on. (since her chest isn't scarred) Hanako may be naive enough to believe a bout of sex is some kind of miracle cure that'd turn their awkward friendship into a lovey-dovey relationship, but I doubt she's so naive as to believe showing your naked boobs to a guy will be seen as anything other than an invitation to have sex. Hisao saw it as an invitation to have sex because that's exactly what it was and Hanako even admitted as much afterwards.
Worse yet, his advances are totally silent on both sides, and you find out Hanako didn't really want to have sex.
Totally silent, but also unambigious. Hanako may not actually have said anything, but her silent nods just before they sat down on the bed and again before the actual intercourse seemed clear enough. The atmosphere was way too uncomfortable for conversation and they both knew it. Hanako may not have wanted to have sex, but she wanted what she thought would be the consequences of sleeping together. Ends justifying the means and all... Even if Hisao could have managed an "are you sure" at that point, the reply would have been "yes". There's little doubt about that.
That may not actually be rape, but it comes really close...
No it didn't. Hanako instigated it, didn't really want the act itself that much, but nevertheless wanted to go through with it.
and it highlights some of the dangers of not communicating openly enough with your lover.
This is actually merely one of the many times Hisao and Hanako failed to understand each other's feelings correctly. It's one of the route's central points. Hisao and Hanako failed to communicate openly throughout the arc. Hisao admitted to Miki he had feelings for Hanako, but because he thought showing romantic interest in her would scare her off, he kept her in the dark about this and friend-zoned her out of misguided pity. Hanako likewise was attracted to Hisao, but was constantly anxious of Hisao interacting with or looking at other females, yet kept those feelings hidden from Hisao so he couldn't explain to her he wasn't actually interested in Yuuko or Miki as a romantic partner. The moment Hanako and Hisao decide to actually communicate openly about themselves is also the moment their relationship changes from a friendship into a relationship and is the conclusion of the central conflict.
Your opinions about Hanako's H-scene are fairly common, but IMHO people are way too eager to see Hisao as some predator and Hanako as a victim. (a practice the whole route basically argues against) It just ain't so. Hanako made a stupid decision and Hisao made a stupid decision in going along with Hanako's stupid decision. Both are at fault, neither more than the other. The result was really nothing more than simply a bad first time. It was embarrassing and awkward but plenty of people in real life have a lousy first time, occasionally for the wrong reasons too and they're generally neither traumatized nor mentally scarred by it, so I don't see why people believe this left mental marks on Hanako in any way...the girl knows what trauma is, this ain't it.
This may seem harsh, but while I acknowledge Hisao failed to grasp Hanako's reasoning during that night in her room, I'm not even upset with him for accepting her offer of sex. In fact, I think he did the right thing and not just because turning Hanako down might have resulted in her feeling Hisao rejected her and had no interest in her romantically. The whole point of the route was that coddling Hanako was counterproductive to her recovery, so it's ironic people are so eager to shield her from the consequences of her own bad decisions instead of allowing her to experience the results and having her learn from them.