Sisko's blaming of Picard is on a purely emotional level. It's easier, after all, to blame an individual than a heartless soulless collective. This can't have been the first time that Picard has met with that reaction either. It is also clear from the TNG episode "Family" that, at that same emotional level, he blames himself that so many died due, in large part, to "his" actions while assimilated. Survivors guilt, with a twist.