Yes. Which is why in some ways he's relieved that she knows - because she may be able to find a way to save more people in Project Ark if she knows what's at stake. She's a Kureshima, after all, why wouldn't she be dedicated to the Project just as he is?

Of course, she wants to stay with Gaim forever, and even if she's somewhat in denial about being able to stay, she's still going to do what she needs to do for them.

(A part of me is glad that Michi's oblivious to Kouta kind of being in love with her. It wouldn't be too hard for her to evaluate the pros and cons of being in a relationship with him, including finding a way to not be a Kureshima anymore.)