The thing was, we already had an episode showing Xander's doubts and fears - "The Replacement" - and that was not one of them. Scruffy Xander, in that episode, was willing to hand over his life to Suave Xander, as Suave Xander, when Scruffy Xander thought he was a demon, was doing a much better job of it. The only reason Scruffy Xander did not give up completely was Anya. If Xander had truly worried about becoming his father, and believed Anya was better off without him, Scruffy Xander would have had that fear, given up and, given his tone at the time, probably killed himself. Instead, he went after Suave Xander with a gun. And we know Xander had been thinking about a future with Anya, in this episode and as far back as "Where the Wild Things Are" so the entire idea of marriage was in Xander's mind, so it wasn't something he hadn't considered.
There was no way that fear would not have been possessed by Scruffy Xander, so it literally did not exist prior to season six. But season six went truly overboard with ignoring the previous five seasons.