Yes, that first one does flow much better. So the full sentence would be:
The one man she would submit to: Nanna the wise, with his many faces, personified to his worshipers as the moon.
Or at least I presume that is correct usage of a colon. No, that is not a request for scat.
In your new sentence 'The one man she would submit to' is still a fragment and does not connect to the rest of the sentence. The main action is his personification not her submission.
you could arrange them together either
The one man she would submit to was Nanna the wise, personified to his many worshipers as the moon because of his many faces.
Nanna the wise, personified to his many worshipers as the moon because of his many faces, was the only man she would submit to.
I would use the word only instead of one.
My advice is always start with the simplest sentence to get across your point and then add to that. What you are trying to say is that 'The one man she would submit to was Nana.' That he is wise or even worshiped is secondary to the point. After you have the sentence that gets the point of the paragraph across then add the 'fluff.'