Well the recent revelation about Kakashi's father pretty much sets it into stone that Jiraiya is most likely the father of Yondaime. A lot of people believed that he was Kakashi's, but that isn't the case.

I still think that the Sannin are around during the Gaiden storyline...so perhaps it will end with the revelation of Yondaime's full name, and him perhaps calling Jiraiya and Tsunade mom and dad?

At least, I think that the Sannin are still here. Although the flashback scenes with Jiraiya telling Naruto how Orochimaru left....he looked a lot younger than the scenes during the old flashbacks in his lab..

I dunno though, like all comics continuity is flexible.