Well a cousin is hardly the same as your brother or sister. And to give their entire race a chance of surviving past their own generation, I think they would do whatever was necessary. Clark sure seemed ready when he first met her in the episode "Kara" and learned she was from Krypton, right up until she said the word "cousin" at which point he instantly backed away from her by about six more feet. But, of course, Clark is growing up with human customs. There are places on Earth where marrying a cousin isn't a problem. Krypton's culture might not have any problem with it. It really depends upon social taboos, and Kryptonian genetics.

The real problem with humans closely related is the threat of losing genetic diversity, and birth defects. However, I'm willing to bet there are plenty of wild animals that by human family trees would be considered "cousins" that have breeded, and I don't see that many three headed horses running around. Again, it comes down to how strong Kryptonian genes are, and if Krypton embraces the same social taboos. Obviously a brother and sister are going to not want to copulate. But two cousins who had never even met as adults before, now facing the imminent demise of their species? It seems like they would be willing to procreate, though they'd probably go to the fortress and look for some high tech way to do it to make sure it was safe, and to satisfy any moral qualms. If Brainiac could genetically alter Lex into a Kryptonian host for Zod, and the Jor-El A.I. could genetically alter a human into a Kryptonian to fool Clark into thinking she was the real Kara in season three's finale, I'm thinking Kryptonian technology is up to the task of making sure the genes of any children are both safe, and modified enough to guarantee diversity.

LOL... when I watched the Superman animated series episode that featured Supergirl for the first time I wondered what Superman's reaction was to when she told them they were cousins. I doubt there's a deleted scene for that episode but then again maybe there is one or some commentary from the writers.

GL (John Stewart) also told Kara: "I don't care who your cousin is" in the first/pilot episode of JLU.

Yeah, that's right. Only their secret identities as Clark Kent and Kara Kent were suppose to be cousins in the DCAU. But Kara was actually from another planet in Krypton's solar sysem, called Argo, that didn't blow up, but was knocked out of it's orbit when Krypton blew. Every thing on the planet froze to death, exept Kara and her family who hid in suspended animation tubes. Everyone else's broke except Kara's and Superman rescued her after getting a distress call.

In JLU, they called each other cousins, and other people do too. I think this causes too much confusion, since they actualy are cousins in most versions.

Oh brother... another thing that'd be crazy if she was pregnant, Jimmy or anyone else within close range of her would probably advise Clark to start running if he said something that ticked her off. i.e. if she was in one of her moodswings.

Doubt Clark or anyone else would wanna be around for that or when she gives birth...

That'd probably be a scream

You know, that may sound silly or gross or whatever, but really it does make sense. Smallville uses Clark's powers as a metaphor for growing up and the physical issues that come with that. Like when Clark developed heat vision because he was getting excited thinking about girls. So it wouldn't be that wrong to show some of the female-only issues that would occur with a Kryptonian woman. I'm thinking something along the lines of Pon Far from Star Trek. Kara gets all hot and tries to jump Jimmy, Lex, Lois, anybody. Knowing she can't get with Clark, maybe she considers opening the Phantom Zone to find a guy or something. But again, that's a bit silly and out-there.