Yes, indeed, trying to argue with a mad man and, of course, underestimating Cardassian sturdiness was a bad move. The moment Sisko realized that Dukat was hearing voices, he should have stopped teasing him and should have thought of an option to incapacitate him or kill him. He should have hidden that fork with a missing tine better and should not have fanned Dukat’s madness.
But it is very easy to say that when you are a viewer. In reality, people act on the spur of the moment and don’t have time to deliberate their moves, very often the emotions and instincts prevail and they do not choose the best course of action.
I do agree that Sisko was in a pretty bad shape after he managed to knock Dukat down. He just departed for the escape pod, probably his instinctive desire to run away displaced the objective of securing his departure. He did not hit Dukat on the head but on the back so one blow on the back, considering that Dukat was wearing body armor, would hardly have been enough to keep him unconscious for a long time or kill him.
Dukat leaving Sisko alive also did not make sense but could be ascribed to his delusion and his fixation on Sisko. Both sides made mistakes, when you have an opportunity to finish your enemy, just do it, don’t talk. But movie combats are not supposed to be realistic.