Off-topic a bit, but one thing I've said about Star Trek in the past is that some of their stories would work really well if they weren't on bloody Star Trek. There was one story on DS9 about a Kardassian soldier who impersonated his former CO (a hated war criminal) so he could be executed in the tyrant's place and atone for his guilt at having worked in a concentration camp. It would have made a brilliant story if they'd set it in post-war Europe, but on Star Trek... well, I just didn't care.
Just to pull the off topic back to the topic...

It's funny you mention this. My girlfriend's never seen
DS9 so we've started getting the discs through NetFlix. We just saw this very episode a few days ago and both thought it was brilliant. We just watched a brilliant one last night about war orphans and custody rights.
One of the best things any created world lets a writer do is comment on the real world. The creators of
South Park have said many times there are so many things they can respond to on their show that would probably get them hanged if these same comments were made on a "real world" show. So not only do elements become relatable, but perhaps they make the reader/ viewer look at things in the real world in a different light.
I've always thought (speaking of getting hanged) that
DS9 was the best of all the
Star Trek shows because it shows all the rough edges of the Federation. It was much more politics and race relations and religous debates than the "wild west" scenario that
TOS,
TNG, and
Voyager all dealt with. Those shows got to move in and out-- here today, gone tomorrow-- but
DS9 had to deal with a constant, ongoing arc about trying to bring a formly oppressed, almost theocratic society into the Federation.
The
DS9 episode you mention wasn't so much about one man's guilt as it was bigotry and hatred. When the epsiode begins, Kira is willing to execute Darheel simply because he's a Cardassian. In her eyes Cardassian = guilty for crimes against Bajor = shoot him in the head (which has no bearing on today's world at all...). As the story progresses, however, she comes to realize this guy's just a guilt-ridden file clerk who feels the same way she does. He also thinks all Cardassians need to be punished for what they did to the people of Bajor. Thus, his own existence proves him wrong--he's a good Cardassian arguing that he should be punished because all Cardassians are evil. Kira comes to realize she was blinded by hatred and agrees to let him go.
...where he's promptly killed by another Bajoran, who insists Darhell deserved it. He was a Cardassian, after all...
That, in my humble opinion, is great storytelling in a very well-constructed world.