Plus, she always gets bashful around him. Nursery scene? Dropping the cookie pan scene? Remember any of that?
Yep. But embarrassment could also explain all those scenes. They are all scenes where, in a normal rom-com the two characters WOULD fall in love after just one scene, that there were multiple such scenes I suggest should put us on guard. After all, according to the title, this is not a normal rom-com.
That last point is ultimately why I doubt the pairing. It is being TOO emphasized, which makes it too plain. Watari is jerking us.
As for the rest of your post, I think all that is true. I just think naruto is afraid to deny Yukino because of what Haruno said about rejection and because he thinks she is dependent on him (and because he understands her family life is bad), and he doesn't want to hurt her. But that would be his misunderstanding.
He respects her and wants to help her, but that isn't the same as being in love with her. He wants to help her, but he isn't as good at reading people as he thinks he is. His cynical nature, accepting that what Haruno said was true, is what he needs to correct in order to advance.