I don't think they're his parents, I mean, Jiraiya is pretty young in the flashbacks, I think, and, of course, the toads aren't people, and can't give birth to people, I'd wager. Besides, we know that the fourth and some rain woman are Naruto's parents.
However, the person that giant toad was talking about was probably Naruto, not Pain. After all, why would it be Pain when Pain isn't truly the head honcho?