[He's confused, too. Kissing her was incredible. He can imagine going to sleep every night with her in his arms (or him in hers, he isn't picky) and maybe motivating himself to make pancakes for her in the morning. There's passion there, too, but it's not overwhelming. It could be written off as hormones or being alone for too long. And, of course, he likes Kitty. She's good to be around, and he likes being able to be there for her. It's a baffling situation.
Whatever it is, embarking on another prison relationship isn't that appealing and Kitty is still in love with Reid. The first problem would be easy to overcome. The second, not so much. Chekov doesn't want to pressure Kitty and he doesn't want to torture himself.
He smiles. It's real even if it's confused and sad around the edges.] Whatever you think that I have done for you, you have done for me also.