I think you are over thinking it... Though in comparing it to the 2005 anime, where she was a lot more clingy near the end, is probably part of that.
I honestly thought that scene, while somewhat unexpected in how it was just "there"... Was actually kind of expected as well. You have to remember, Sho has always had a thing for her, and they have been in a tight group for the past few years, where in, Sho has saved her and her brother multiple times. I think after he reclaimed the Guyver to fight Aptom, to save her, that she was a lot closer and developed more solid feelings for him specifically.
So I found it as an obvious progression. Sure, it wasn't handled well... It is a Monster/Action manga in the first place... But, I think that was just a simple nod to everyone who may have wondered if she was still not his girlfriend... Which she clearly is now.
So, while they may never have a serious relationship talk, or even kiss in the manga... We pretty much know that they are a couple... And I think it isn't in her character to just be sleeping with Sho for no good reason.