Would Sisko really put his spiritual journey over the well-being of his children? Having seen how teenage Jake completely fell apart the last time he disappeared, I really doubt that Sisko would be eager to abandon him again. Not to mention abandoning his new child even younger. Plus it undercuts Sisko's character progression throughout the series. When we first see him he's still agonizing over the loss of his wife, and over the course of the series he finds a new love and starts a new family with her. He finally has the chance for the happily ever after that he lost at Wolf 359. That, plus the racist trope Brooks had asked them to avoid, means that Sisko's choice never worked for me. YMMV.