One need not be Mary Sue-ish at all, the term "Mary Sue" is generally slapped on a character who is important in the story, possesses unusual physical traits, and has an irrelevantly over-skilled or over-idealized nature.

I don't see a demi-god with a highly advanced intellect being Mary Sue at all. If that were so Einstein would be consider Mary Sue because of his intellect compared to normal humans. Fenyman would also be considered a Mary Sue for his ability to conceptualize problems via direct characterization, and his IQ was a "mere" 125...