It's the worst because it completely undermines one of THE cornerstones of DS9 (and one of the most important aspects of DS9): Sisko being a great dad.
Sisko willingly allowed his son to stay possessed without trying to rid the Pah-wraith. He was risking his son's life for that battle, and he is watching Jake getting hurt and bleeding and was just standing there. This goes against everything we have seen of the man for those past 6 years, and is just a monumental insult to his character. It's the only episode that actually does some character assassination of him
When Kai Winn looks like the hero and the reasonable person by the end of the episode, you know you screwed up badly.
"THE RECKONING" is one of the ONLY episodes in the entire franchise that gets worse with every rewatch. It used to be the 6th or 7th worst... then 5th... then 4th. Until it finally replaced "PROFIT AND LACE" as the worst.