The chances that Sora, Sanji's mother, and Sora the hero are unrelated is close to zero. Unless Sora was one of Judge clone experiments (and he picked her name out of spite) OR she was a descendant of the actual hero (and he married her out of spite), it is likely the hero of the comic strip was named after her.
And neither of those "spite scenarios" makes much sense to me. Sora being a clone would make sense but I doubt he would name the Queen of the Germa Kingdom like their greatest enemy, he would be insulting his ancestors for petty reasons. Judge marrying someone out of spite would be in contrast with his goal of generating the most powerful enhanced humans ever, even though it would be fitting for a Romeo-Juliet parallel.
This being said, there are only two reasons someone would create a story where someone named Sora is the hero: either you hate Judge and Germa for what they did to Sora or you are Judge and you regret your action. Since Judge knows Morgans and he doesn't seem to resent him, I would exclude the former.
I also can't bring myself to accept Judge as fully evil. Sanji looks exactly like him in the future where things went wrong.
Deep down, I'm convinced Judge is a kind guy. A man who had to carry the full weight of his ancestors' dreams on his shoulders and lost everything -even himself- in the process.
Judge being the artist behind the comic strip would make for a great twist, imagine if drawing meant to Judge what cooking means to Sanji. What a beautiful and tragic story