I really liked the Nea story-line, and was glad that being friends with her meant something (there was a similar situation in Mid Life Crisis, but the relationship with the trans-girl there was pretty much a non-thing if you didn't want to have sex with her). But for the developer to go "either you have to be her lover, or she kills herself", that is a straight up dick move from a story telling/ game making perspective.
And it really smacks of what people have done in real life as well "If you don't love me, I'll kill myself!" And some do it too. That is deliberately done to cause guilt in the other person, and is a dick move. Here Nea didn't try to guilt the player, the Dev did.
Honestly, Nea going off the roof is an unfortunately realistic decision, and given her history, a likely one. BUT, and this is the important part, it would probably have happened before the MC got back no matter what. The mistake there was not whether he wanted to be her lover, but that he ran away after catching her masturbating, especially knowing her history. Thus she most likely would have died no matter what the MC decided.
To be fair, the character is 19, which means he still hasn't received his brain in the mail. I'm decades older than that, catching someone jerking off would only barely phase me now. "Oh, oops, sorry, didn't mean to interrupt. I'll wait."
It isn't hard to realize she is going to be mortified, but given her history she is likely to think that you hate her now and that would be very bad. So really, that entire conversation should have been immediate, and with the MC trying to figure out what he wanted on the fly. The conversation may have been through a bathroom door.
But, if you're going with the MC runs away and then comes back in the nick of time to prevent her going off the roof, you should have that happen either way. Getting caught masturbating is not grounds for suicide. And she needs a friend more than anything, she can find a lover once she is out of school and can connect with people in the wider world - I'd recommend moving to a bigger city though. So in the friend route you tell her that you don't hate her, you don't think she is a freak, you have no intention to kink shame, and you still want to be her friend. And who know what the future may bring? I hooked up with a girl 30 years after we first met as kids (didn't last, but that is a whole different issue).
So I agree that she should be left in the story as a friend. Maybe not much direct interaction - although can still be a catalyst in other relationships - and be there in other scenes, like the bonus scene with Eve. She still there, she is still your friend, you still let her keep her 'girl stuff' at your place and let her change into and wear it from there. And she still has a chance at happiness.
And who knows, maybe in time the MC might decide he wants more. Or if she gets reassignment surgery and the elephant trunk in the room is removed - and a vagina added - then that sole impediment may be enough for them to be able to be together as she wishes.
Side point, it is a credit to the dev that the character of Nea is such that a bunch of us care what happens to her - a fictional character. Heck, for me, in many stories (not just porn, I mean regular movies, TV and books too) when they get into the 'character building' I hit the fast forward button.
A related thought to getting caught jerking off. Something similar happened in my school (many MANY moons ago). Wasn't a trans person, just another kid. He (supposedly) got caught jerking off into a sock in the boys change-room. The story went around the school.... and after a relatively short time (certainly not three years) it blew over and everyone went back to not giving a shit. I also say supposedly because just because some kid SAYS he saw another kid doing something, doesn't mean it is true. So if people were still bullying Nea over it three years later, it had little to do with getting caught jerking off - even if sniffing someone's underwear - and far FAR more to do with being trans.
Clearly this school has a shit bullying policy. Which is sadly normal in the real world.
I found it interesting that when the MC catches her masturbating, she wasn't jerking off, she was playing with her butt. This matches up with what a psychiatrist told me once (in a discussion from years ago), that trans people often feel their sex organs are wrong and do everything they can to de-emphasize them. Not always of course, but often.
Thus they may not use them when pleasuring themselves, but try to do it as the gender they see themselves as does. A t-girl like Nea would rub her breasts and butt, maybe leave her underwear on and rub her crotch as if she was rubbing her clit. Not sure how a t-boy would go about it, maybe get a double headed dildo that when inserted he can jerk it and it will rub around inside and against his clit (there are strapless ones made now that are meant to look realistic and be used as if the girl has a penis, although apparently they are a pain to keep in place, so they often wear nylons with a hole in them to keep it in).
The point being, Nea may not even WANT the MC to touch her penis, because girls shouldn't have one.
Yes, yes, trans girls in porn use their dicks all the time. Never use porn (or movies, or TV shows, or fiction books, or video games, or Facebook, or YouTube...) as a source of information for how things work and people act in the real world.
Anyhoo...
I also had an amusing thought about another way to do a relationship with Nea. Through Heather.
Now that Heather is becoming sympathetic towards Nea, and knows that Nea has it bad for the MC, but the MC is unable or unwilling to go further, then Heather could be the bridge. The three of the play together, and Heather will be the one that takes care of Nea's penis during those times (assuming Nea would want that).
As a final point, I thought the scene with Nea giving the MC a BJ was really hot. She is cute, no matter what.
I was surprised she didn't pull her little dick out and jerk it at the time though, or quietly jerk off next to the MC in bed that night - the player can be given a choice to just quietly pretend to be asleep, or caress her as she does it. You'd think at that point she would need to get off, bad!
Of course, there is the above mentioned issue, so hard to say if she would want to.
Well, that's my quarter (inflation, it's no longer 2 cents).