I love Hard Time too much to delete it from canon, but I agree that it's a major problem that it didn't have lasting ramifications. I see it as an example of a fault in the nature of episodic storytelling more than as a fault in the episode itself. Of course, DS9 was much more linear than other Trek series, but it had it's episodic moments and this one often comes to mind. On the other hand, I can accept The Inner Light a little easier. I can tell myself that, since the objective of the probe was a positive one, maybe the effect on Picard's mind was different and the details of the experience faded soon afterwards, like a dream. That doesn't work so well with Hard Time because it's made abundantly clear that the experience had lasting effects.
As for an episode that I would delete, I can't think of anything off the top of my head from DS9 that I feel has to be eliminated. As for Voyager, Threshold of course and Endgame. Aside from my general opposition to all the technological upgrades Voyager got, there's also the matter of having a Borg transwarp conduit right next to Earth. That puts Borg competence into serious question when you wonder why they haven't just flooded local space with cubes.
If I were to get more heavy-handed, Enterprise would be up for a serious culling. Unfortunately, if I go down that lane I'll end up just discussing how I would have done everything differently rather than simply eliminate some things from canon, so I'll just leave it be.