It's likely that the ships we saw being destroyed so easily had already taken some damage, possibly from their invasion of Cardassia but almost certainly from the first barrage of fire from the station itself. The station unleashes a massive amount of torpedo fire very quickly and it's several seconds before it cuts to any ships actually being destroyed...and that's mainly just from the vantage point of a small handful of launchers. The station had many such launchers and was firing bursts of torpedoes almost nonstop from half of them.
When Sisko finally orders the switch to phasers, it's likely that a good number of the ships in range of the station had already taken at least some damage. Those BoP that were taken out with one phaser shot had likely taken heavy torpedo damage already.
Granted none of the ships appear to be damaged in the least before being blown apart, to say nothing of their apparent lack of any defensive shielding. But there was simply too much weapons fire coming from the station to assume that when we saw a ship being destroyed after taking one or two shots, that in fact those were the first hits they had taken.
And as others have said, the station would be sporting larger starbase grade weapons. The mere fact that the stations torpedo launchers were firing so rapidly lends credence to this. And while no one said as much on screen, given the technological superiority of the Federation and their alliance with the Klingons, it stands to reason that Starfleet would know how to exploit whatever advantages might be available against the Klingon ships, just as Riker and Data knew in Generations to exploit the age/weakness of the BoP attacking the Enterprise. (though the mere fact that Riker and Worf allowed the BoP to inflict such severe damage to the Enterprise, is beyond negligence and neither of them should be allowed to step foot on a Starfleet ship again, even after they get out of jail...but that's a topic for another time.)