Second off, my theory:
There's a lot of questioning about Winry at the end of this episode. I know for a while I thought she was Envy, too. Then I rewatched it and her smile isn't Envyish. I mean, even when he was Gracia, his smile was more devious, and here it looks sincere.
I'm aboutu 50/50 on if she's real or not. But I think if she is, she's smiling because of how much the boys have matured, or something along those lines.
Third off, pimpage. My friend created a new FMA community. So now I'm pimping it for her. haganenokokoro.