Troy is the better of the two. Donna isn't Greek -- and I don't think most people recognize Troia as being a Greek word. Even people not familiar with Greek mythology have heard to Troy thanks to the Trojan Horse story. And since it's her last name, I could see people just referring to her as Troy the way military refer to people by last names in battle.
I think they need to abandon the connection to stars altogether. It doesn't fit if she has her classic origin (which is better than the post-Crisis version).