He knew all that while being held captive on Zod's vessel. There was no choice at that point. It was already made clear that Zod isn't to be trusted. Zod was already in the process of terra-forming Earth. Zod has already threatened Earth and the people he loves. Trying to have some dramatic pause in the conflict just didn't work for me because of what was already at stake. I don't believe Clark cared at all about Krypton or it's possible future. The reason I think he cried out after killing Zod was the simple fact that Zod forced him to take a life not because he killed a fellow Kryptonian that until recently knew nothing about.
All he knew was that Zod was going to terraform the earth, not how he was planning to repopulate it. Or he could have protected the ship earlier (or destroyed it).
Even if he did know, it's still a completely different thing when you plan something of this magnitude to the point when you actually do it. His pause, clearly shows that he handn't thought about it like that at all.
And of course Clarke cared about Krypton. That's who he is, Kryptonian. Hence his delight when he found out about his heritage. The whole film is about how he is struggling to fit in to Earth and it's population. It's him trying to find an identity as an outcast, an alien species. He doesn't know who he actually is or why he is on earth until he meets his Holofather.
The moment when he pauses is the moment he chooses to fit in fully because it is the moment he wiped out his own bloodlines, his own civilization to protect those who were adopting him. He fulfilled his fathers wishes by trying to lead the people of Earth, and by saving them.
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