The idea that Sisko couldn't see beyond his prejudice undermines his ability to be a competent leader. He obviously couldn't be seen to be incompetent from the first episode so it was written that way for another reason.
Well, here's what the Wikipedia guide to the episode says:
Sisko is resentful of the duty, having lost his wife Jennifer three years previously during the Borg attack at Wolf 359 and destruction of his former ship...Sisko becomes more despondent of the position as he gets his final orders from Captain Picard, the man Sisko holds responsible for Jennifer's death...
the entities point out that he continues to return to the moment of Jennifer's death. Sisko comes to the realization that he has been grieving over the loss of his wife and explains this to the aliens.
When the Enterprise arrives in response to Kira's earlier call for help, Sisko informs Picard that the wormhole aliens have helped him to overcome his grief about Jennifer's death and to move on, and that he plans to remain station commander indefinitely.
From memory alpha:
The conversation [between Sisko and Picard] is dominated by thinly-veiled hostility on Sisko's part, as he faces the man he holds responsible for the death of his wife.
Sisko confesses he's never been able to get over losing her and that inside he does still exist here. But finally Sisko realizes that Jennifer is really gone and he has to let her go forever. He leaves the quarters again, but this time he walks away finally leaving the trauma of his wife's death behind him.
So I'm really not sure what you're taking issue with. But maybe you could, you know, say what you think the reason is
instead of just saying what it isn't.