I'm going to play arm chair psychologist for a bit so bear with me.
I think that of all the "O'Brien suffers" episodes, Hard Time and Whispers are the two most difficult to enjoy, especially if you're an O'Brien fan.
It's not as though we don't see other episodes like this. Tribunal, Visionary, Honor Among Thieves, The Assignment and Empok Nor are other episodes in which O'Brien is put through the ringer. However, in those episodes, O'Brien always triumphs in the end and comes off looking heroic.
Hard Time strips him down to a point where he becomes suicidal. The only other character we see go through that type of emotional torture is Garak while he's decrypting Cardassian transmissions. Whispers takes it farther and ends with the O'Brien clone being killed. It does feel wrong that this being is put to death, basically for nothing, since he never even tries to complete his mission.