Sometimes tears are joyful, remember that. I have frequently cried at overwhelmingly happy moments in stories. SukiMega, as fluffy as it was, could get me like that sometimes, I think? Many climactic moments in romantic stories have gotten me teary-eyed because I was just so happy it finally happened.
And yeah... this is definitely a step in the right direction. Kyo still has his own self-esteem issues to gradually work through, but he can at least acknowledge there's more significance here than he's been willing to admit before.
Don't expect him to suddenly make a grand move overnight, for instance. He's probably one of the most considered, methodical male leads in manga, and he needs to be absolutely sure he's ready for that step by making many smaller further steps.