Most fans, myself included, hold the Hama comics to be the official canon of G.I. Joe, but some characters just worked better in the animation, either because of their personalities, origins, or because Larry wanted as little to do with them as possible. I'm inclined to think this was the case with Serpentor.
Larry tried to keep the comic as grounded in reality as the concept permitted, and the sort of genetic engineering that was required to bring Serpentor to life was a bit of a stretch.
I have no idea who came up with the "idea" for Serpentor, or his basic backstory, but my guess would be that, since there was no particular correlation between the animated series and the comic book, apart from them both presenting adventures of the G.I. Joe team vs. Cobra, that both were given the basic outline of Serpentor, told to make him a major player, and went with it from there.
Ultimately, I do think the story worked better in the cartoon. But I think both the animation and the comic book handled it well enough within their respective universes. Let's face it, the animated series was always a somewhat wilder and less realistic environment. That didn't mean it wasn't fun to watch!
