This is a long thread, and I've only read a couple posts, so forgive me if someone else has already mentioned this.
I think the tipping point for Sisko deciding in Pad'ar's favor goes back to him agreeing to Sisko being a mediator to begin with... he is a father.
Ben may very well have thought, "What if this happened to me? If Jake was taken and I was led to believe he had been dead for years?"
More than anything, Sisko would likely understand Pad'ar's pain and he saw how happy he was that Rugal was alive. Given how strong and great a father Brooks portrayed Sisko being, it's actually pretty easy to see how this decision happened.
The fact Pad'ar made that comment to Sisko before the start of the hearing was foreshadowing of Sisko's decision. At least, I always felt that.
Regarding the comparison to Picard's decision in "Suddenly Human", he was never a father. Plus, both of Jono's parents were dead, as well as most of his family line. In many ways, it's the exact oppisite scenario as "CARDASSIANS". So I am not sure it's fair to compare the two, though it is very easy to do so.