Well, I think that the main problem is the fact that Clark still seems to be stuck on the idea of finding his 'soulmate'. And he worries that Lois isn't his soulmate, but that he will be stuck with her because of what has happened in his marriage to her:

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One of the messages from Jor-El said Kryptonians mate for life, but I don't know what that means or if it matters what that means. Does it mean that I've... turned her in to my soul mate or whatever by marrying her or by sleeping with her or having babies with her? Or does it just mean that there's no such thing as divorce on Krypton?"
Clark does not feel that Lois is his soulmate, and he wants to find the woman who is. He used to think that Lana was the one, but Lana basically told him here that the two of them don't have a future together. And because Lana won't be his soulmate, Clark is still stuck on finding the woman who is. Why else would he want a divorce? He has no other woman who waits for him, not really. If he leaves Lois, he has nothing and no one to go to instead. The only thing that makes any sort of sense to me is that Clark wants to find his soulmate, and he doesn't feel that Lois is the one.

Good conversation with Van-El. I thought that Van-El would drive me crazy, but he didn't. He told Clark some useful things about Krypton. Like, if Clark had still been on Krypton, his parents may have married him off to someone who wasn't his soulmate at all, and he would basically be stuck with her. Or he might have found his soulmate and been unable to marry her, because the two of them belonged to different social strata. So stop living such a pipe dream, Clark!

I agree with those who say that a bit of shock therapy is just what the doctor ordered. Let's see what the launching of the Messenger will do to Lois and Clark.

Ann