You're right that he didn't choice between Jonathon and Lana exactly. But he did allow someone else to die to save Lana. There was no question that he knew another loved one was at risk if Lana is brought back to life.

I would understand wanting to save Lana if there was still a chance of that, as in her still being around but badly injured say (Like Martha was). But Lana was already dead when Clark made his deal, which is when it became about reversing time, and bargaining with the life of another