Kashimashi: Girl Meets Girl
Hazumu got turned into a female because Hazumu had already identified as one.For the most part Hazumu is much happier as a female. The fact that it takes so little time for Hazumu to adjust to the new identity and that Hazumu is very naturally feminine is further evidence of Hazumu identifying as female. Finally, the fact that Yasuna can see Hazumu even when Hazumu was in a male body is extremely likely to be linked to Hazumu's gender identity. Finally when the aliens reconstructed Hazumu's body, they have enough Magic from Technology to draw directly from Hazumu's spirit. Since Hazumu's spirit identified itself as female, the Magic from Technology reconstructed her body as such.
Ayuki is in love with TomariYou know all those times she was talking about liking someone but not chasing after them and such?
Ayuki is in love with YasunaShe is extremely sweet to Yasuna in the manga when Hazumu ditches Yasuna for Tomari. Maybe they even get together, which could explain why Yasuna seems to be taking it so well, even though it it never explicitly stated.
Tomari had a slight crush on YasunaEver so slightly, in the manga. Most likely she didn't even notice
Yasuna had a slight crush on TomariYasuna swoons over Tomari a few times, especially when Tomari behaves more "girly", so who knows what would have happened if Tomari had decided to do that more often. It sure does explain somewhat why Tomari and Yasuna were still rather nice to each other, despite them competing over the same girl's affection.
Everybody is polyamorous and in love with everybody elseI figured I'd just combine all the other theories we've seen here.