@Darudius As far as I can understand it, judging from the facts:
[ul]there's the known analogy with "the moon is beautiful" "tsuki ga kirei" meaning love
and the fact that Koto steals the moon to give it to Kousuke
that she tells him he can keep it in his heart to make his life without her less painful
that they reiterate their feelings to each other
that Kousuke says he has his public life continue on like normal
but that his true self is carrying a (quoted) "secret" between him and Koto, in his heart[/ul]
I think they'll see each other sporadically, like, not too often, maybe at the café where she works, maybe not (because there seems to be an implication that maybe there's a court order disallowing him to see her for a while, I'm not 100% sure on that one, but I wonder why he says it's against the rules to see her), and keep on living their lives separately, while still loving each other, so... I think it's fair to assume they'll rekindle when it's legal and safe for them to do so.
There's no guarantee ever, but yeah, I think it's a beautiful ending. It's a bit vague, yet not hopeless, not 100% hopeful either. I think it's a fitting ending for the manga.