I think it’s just an insult–the ultimate insult a man can receive, since it questions his very manhood and places his relationships in jeopardy. We’ve seen nothing of Rumple’s marriage and no reliable source has yet commented on it, so for now I’d say we should reserve judgment. Besides, if there was something to the statement, Regina probably would’ve heard about it at some point and would’ve made a dig about it. Instead, she doesn’t seem to even know Rumple had a son, which suggests to me that the remark was just something the guard made up on the spur of the moment. If it had become a public rumor, it would have become part of the Rumple legend and Regina would’ve heard it.
Even if it were true, it doesn’t seem to have affected Rumple’s relationship with Bae. I don’t think anyone could say he loves the boy any less.