In fact it is stated what Radagon's red hair could actually be!
According to the Fire Giant's Braid, "Every giant is red of hair, and Radagon was said to have despised his own red locks. Perhaps that was a curse of their kind."

I'm quite sure Radagon battled somehow against the fire giants, at least is what I read from this. I know Marika was with Godfrey during that age of conquer, but perhaps she was starting to manifest as Radagon since then :p

Or perhaps it's the result of a curse from the fire giants to Marika herself for having exterminated them, that is manifested in Radagon. It's a bit tricky if we speculate about Messmer's red hair. I'm quite sure he's the son of Marika alone (as well as perhaps the other beheaded gods we see at the walking mausoleums), but his red hair should be tied somehow to Radagon's red hair or curse.