Well written, moving story.
This is a concept that I can truly buy into. No matter how much they may love each other, Lois could never live in the fishbowl that would be the life with a public Superman. And that doesn't even consider the danger that she would constantly be exposed to.
The reason given for the secret identity had always been that Clark wouldn't be able to have a 'regular' life if everyone knew. But if would be worse for Lois. She wouldn't be able to have any life. As mentioned, she would have to be shut away some where, never being able to do anything, or go anywhere, without him. She'd have to live her whole life only with and for him. As much as she may love him, this would kill Lois. She would not only lose who she is, but she would have no existence without him. Her spirit would die.
Instead, she had to choose to live with the pain and make the best out of a life where she could still be who she is. In a way, this shows us that Lois is indeed the stronger of the pair. They are in a nearly untenible situation, but she has taken the initiative to make a choice, while Clark merely waited, hoping she'd come up with a miracle solution.
She made the tough choice, and decided that a somewhat less happy life was better than no life at all. Clark is now 'forced' to finally confront what he knew all along was inevitable.
I wouldn't put much stock into the 'John Tempus' thing. I believe that was merely a tongue-in-cheek wink to the gentle readers. But who knows...?
Tank (who thinks that Clark's only choice is to become a hedonistic playboy and have meaningless flings with super models and starlets...the poor bastard

)