If a
girl is
beautiful you should tell her so.
If both you and said girl are mature enough to appreciate true beauty there should be no problem. The comment is just what it means: "I looked at you just now and thought that God must be a fucking genius to have created you and placed you on this Earth." No more, no less.
If you are with a woman but you are afraid to tell her you think she is beautiful, perhaps you are not with the one you should be. If she cannot appreciate the fact that you think she is pretty, and rather automatically believes that you are with her solely for this reason, then this isn't a relationship that needs any more of your attention.