For what it's worth I completely agree with you. I think there are three episodes that annoy me like that:
- Sons of Mogh for the reasons you mentioned.
- Hard Time: Being in some sort of mind prison for decades
is going to alter your personality and leave psychological scars. They dealt with that way too casually.
- In the pale moonlight: Didn't agree with what Sisko did, didn't agree with him getting away with it with no further consequences, didn't agree with his "I'd do it again" at the end of the episode.