I think you're right, Dragon, that Clark was overwhelmed by the idea of not being the last Kryptonian. I think he also felt duty-bound. Zara appealed to his sense of duty, and that is a very effective motivation for Clark. So I think the way for someone to help him see reason would have been to appeal to a higher duty.
He also needed someone to help him think clearly about the implications of accepting the duty that Zara was presenting him with. If he is the only one who can save New Krypton simply by virtue of his birth into the royal house, the obvious implication is that the only way to ensure the continued stability of the government is to produce an heir. Was he really willing to do that? And to stay there to raise and protect him?
But since Clark has the world't biggest Messiah complex, he wouldn't have been able to reject Zara's demands unless he could offer her another solution. I don't know what that might be. What those New Kryptonians really need is a revolution. How did these ruling houses get established in the first place? At some point there must have been some struggle for power and certain families came out on top. What Zara is trying to avoid is a crisis of succession and the resulting civil war. What if EPRAD could help Zara find a more hospitable planet? Then the house of Ra could claim supremacy by right of conquest/discovery or some such machination?
