[Nate the Great]

SISKO: How did you come to adopt him?
PROKA: My wife and I felt that Rugal shouldn't suffer for crimes committed by others.

The plot falls apart here. Raising Cardassians to hate other Cardassians sounds like spending a lot of time and resources (neither of which Bajor has in abundance) on something that would be at best a nuisance to the Central Command and at worst an excuse for the Cardassians to come back and reoccupy the planet.

SISKO: But why would he attack another Cardassian?
PROKA: That Cardassian should have minded his own business.

You didn't answer the question, Proka! At least come up with a nonsense explanation that Garak seemed threatening!

SISKO: The Cardassians are suggesting that the Bajorans are raising these orphans to hate their own people.
PROKA: To hate Cardassians? It shouldn't be too hard, should it? We told him the truth, Commander. The truth about what Cardassia did to Bajor.

A key issue here is that racism is NEVER justified. Ever. Furthermore, Cardassia didn't occupy Bajor, the current government did. And as I've mentioned before, Garak himself never actually oppressed the Bajorans, he wasn't even in the sector until he bungled the mission that led to his exile. Even if you can justify "only hate Cardassians in the military" (which you can't), Garak doesn't qualify.

SISKO: There'll be ample opportunity to go over the matter in detail, but during the investigation, we'd like for Rugal to stay with our schoolteacher, Mrs O'Brien. She's expecting him now.
PROKA: What if I refuse?
SISKO: Then I'll have to call Security and have them remove him from your quarters. I don't think either of us wants that.

I know that it has to be the O'Briens to make use of the cast, but it still doesn't make sense. Unless you're going to tell me that the O'Briens are the only non-Bajoran family on the station, which is extremely dubious. Frankly Sisko himself would make a better guardian right now.

BASHIR: Gul Dukat. He called Commander Sisko right after this happened. Apparently he was quite concerned with your well-being. You never mentioned you were friends.
GARAK: (laughs)

From Garak's perspective this would indeed be a funny joke, but the benefit is that we viewers can laugh harder and harder with each watch as we learn more about the series.

GARAK: Tell me, Doctor. Is there a single trait would you ascribe to me and to my fellow Cardassians? Would it not be our attention to detail? Do you think we simply forgot about those poor little orphans when we left Bajor? Do you think they simply slipped from our minds?

While I'm not a fan of single-adjective descriptions of alien races, Garak does have a point.

DUKAT [on viewscreen]: I did not choose to leave them behind, Doctor. I was ordered to leave them behind.
BASHIR: Ordered? By whom?
DUKAT [on viewscreen]: By the civilian leaders. They
BASHIR: Excuse me, but if I understand the Cardassian political system correctly, the civilian leaders have no direct authority over military officers.
DUKAT [on viewscreen]: Who's been tutoring you in Cardassian social studies, Doctor?
BASHIR: Your old friend, Garak.
DUKAT [on viewscreen]: Well then, perhaps you should remind my old friend Garak the withdrawal of Bajor was a decision made by the civilian leaders. One that I clearly opposed. And yes, they made the decision to leave the orphans behind. A decision I've regretted ever since.

The precise relationship between the Detapa Council and the Central Command is a screed by itself, but the short version is that the military lets the civilians think they're in charge, while pulling the strings to make sure things never get too bad for them. In the case of Bajor, it was decided that the planet didn't have enough resources left to make it worth fighting over. No doubt Dukat didn't agree with that assessment, but he's hardly the most objective member of the military.

As for leaving behind the children, Dukat didn't actually answer Bashir's question. Given later revelations about Bashir's genetic modification, this seems absurd. Don't tell me that Gillian Taylor has better memory recall than an average Academy graduate!

BASHIR: He's lying.
SISKO: Is that an opinion, or do you have evidence to support it?
BASHIR: I have Garak.
SISKO: Garak.
BASHIR: He seems to think there's more going on here than we realise.

You have to admit that while both men lie to their benefit, on the whole Garak actually lies to benefit Cardassia (or at least his idea of Cardassia) and Dukat lies to benefit himself. This is a big difference.

DAX: Why would Garak want to undermine Gul Dukat?
BASHIR: I'm not really sure. I don't think he likes Dukat very much.

Another interesting question. Garak wouldn't actually hold Dukat responsible for war crimes against the Bajorans, as that was the position of the government at the time. Garak hates Dukat for being self-obsessed to the point of being a danger to Cardassia.

KEIKO: She's asleep. She and Rugal played all afternoon. He wore her out.
O'BRIEN: You let them play together?
KEIKO: Why not?
O'BRIEN: The boy almost bit somebody's hand off.

I'm confused as to why O'Brien is being this stupid. He knows that Garak's "crime" was being a Cardassian. A racist reason, but still a reason that doesn't apply to Molly. If O'Brien was still that racist against Cardassians he wouldn't have let Rugal into his quarters to begin with.

The more I think about it, there are enough dramatic possibilities for two episodes here. Wouldn't there be one Bajoran faction willing to throw Rugal to the wolves (Cardassia) to maintain peace and another who would be determine to keep the orphans in order to breed an anti-Cardassia army to defend the planet against the next Cardassian invasion?

O'BRIEN: Gentle was bred out of these Cardassians a long time ago.

A huge misstep. I would've thought that during his self-revelation back in "The Wounded" he would've learned to stop painting all Cardassians with the same brush.

KEIKO: You know, that was a very ugly thing you just said.

Yes, it was.

RUGAL: I want to go home.
O'BRIEN: He'll understand that. You're a Cardassian. They should've taken you home when they left.
RUGAL: No, I mean home. To Bajor.
O'BRIEN: It must be tough for you, living on Bajor.
RUGAL: Why?
O'BRIEN: Being Cardassian.
RUGAL: That's not my fault. I was born that way.
O'BRIEN: That's not what I meant. There's nothing wrong with being a Cardassian.
RUGAL: Yes, there is.
O'BRIEN: Who taught you that?
RUGAL: It's the truth. Everybody knows it.
O'BRIEN: How do your parents feel about Cardassians?
RUGAL: They hate them.
O'BRIEN: Why would you want to live with someone who hates you?
RUGAL: They hate other Cardassians, not me. My parents have never done anything wrong to me.

This is a serious logical disjoint on Rugal's part. Blanket racism is okay, but localized "unracism" is okay. Furthermore, teaching to hate would qualify as "something wrong".

O'BRIEN: Well, you can't judge a whole race of people. You can't hate all Cardassians or all Klingons or all humans. I've met some Cardassians I didn't like, and I've met some I did. Like you.
RUGAL: Do you know how many Bajorans the Cardassians murdered during the occupation? Over ten million. We had a test on it in school. I wish I wasn't Cardassian.

Another disjoint on Rugal's part. And like I said "Cardassians" didn't murder Bajorans during the Occupation, the military did. At the order of the government, granted, but still, not "all Cardassians."

BASHIR: It's Garak, sir. He wants to go to Bajor.
SISKO: Bajor? For what?
BASHIR: He wouldn't tell me.
SISKO: Oh, well, by all means. Will one runabout be enough?

We needed some humor at this point.