They could even had stood to do a little more of this on DS9. Yes, it was a lot darker than TNG; yes, the character development was arguably a lot deeper; yes, it had those long, complicated story arcs towards the end of the series. And yet...you have In the Pale Moonlight...you know, the controversial episode, the one that some people criticize for deliberately flouting Roddenberrian ideals.
I don't mind so much the darkness of it or the deliberate ideal flouting, etc., but I wish that the personal ramifications for Sisko had extended beyond this episode. I don't think it would have taken anything away from his character to have him continue to struggle with his conscience over this, to have him say, once or twice over the remainder of the series,"Hmm, I thought I could live with this, but it's turning out to be more difficult than I had anticipated." In fact, I think it would have even deepened his characterization because, like I said before, that kind of stuff follows you around, and the more you'd like to put it behind you, the more it keeps coming back to haunt you.
In the interest of full disclosure, I should say that I don't like Sisko. I mean, as an analytical former English major, I appreciate his complex characterization, but as a fan, I personally don't like him.
First strike against him was this unreasonable grudge that he held against Captain Picard.1 Any decent person should understand that Picard was captured, forcibly subdued, profoundly violated, robbed of his very sense of self and used as a weapon against his will, but Sisko acts as though Picard had willingly collaborated with the Borg.2 Talk about blaming the rape victim.
Then there was the forementioned "In the Pale Moonlight," in which Sisko does something terrible, betraying both Federation values and his own personal moral code, feels bad about it for all of forty minutes,3 then he promptly gets over it. And unlike the assimilated Picard/Locutus, he did it all of his own free will. Strike two.
Then at the very end, he leaves his pregnant wife behind to go gallivanting off with the Prophets. If the Prophets are really outside of linear time, couldn't they just take him off to do whatever the hell it is they're supposed to be doing and then put him back at the exact moment that he left? So that instead of saying good-bye to Kasidy4 he could just come back and say, "Hey, honey! Guess what I've been doing outside of linear time!" No wonder she's such a hard-ass on Castle.
That's strike three, Sisko, and I know you know what that means.
1To be fair, my own past experience as Locutus of Nigeria colors my feelings toward Sisko in this matter, but still ....
2I'll just take this moment to point out, yet again, that Captain Janeway DID willingly collaborate with the Borg, and her punishment for this act of treason was ... to be promoted to admiral. And for some reason, everyone is okay with that.
3Yes, I know he says at the beginning that he's been agonizing over it for two weeks, but we only get to see 40 minutes' worth of intrapersonal struggle.
4Speaking of Kasidy, note how Sisko totally just forgives her for knowingly and willingly running supplies for the Maquis, yet he holds Picard responsible for the death of his first wife. I know, character development and all that, but come on.