First off; its rare that you and I are on different sides of a debate. This is fun.
Secondly; Im not saying SO is a good story. Its easily the worst origin, and one of the worst stories, I have ever had the misfortune of reading. If I had my way they'd be using Morrison's Action origin, or failing that the pre-Metropolis material from Birthright. Left to my own devices I'd have DC buy every Secret Origin discount-bin floppy issue and trade collection and launch them all into the sun, because I dont even want the ashes left on this planet.
However, its going to be SO, and all Im saying is that Superlad is right and there *might* be a silver lining, assuming the creators keep going in the same direction they have been.
SO was the last official origin in post-Crisis. So this is the origin that Superdad has had since his return; we're just now finally cementing the fact. And the books have been good (at least Tomasi's Superman anyway) so clearly using SO isnt hurting the quality.
Think of it like the marriage. On a conceptual level the marriage is fine. But 90% of the actual stories were beyond terrible. It brought out the worst in Clark and Lois both as individuals and as a couple. Yet despite that background (which would imply that these two should've been divorced by now!) Tomasi has made it work just fine, and because the marriage was already "built into" the characters, Tomasi could just hit the ground running with it.
Secret Origin, on a conceptual level, is just a list of pre- and post-Crisis elements Johns threw together. The actual story was beyond terrible and played up the worst stereotypes of what non-fans think Superman is. But despite that it still offers plenty of material for Tomasi to use without being too restricting. Clark and Lex knew each other briefly as kids. Clark had adventures with the Legion as Superboy, the Kents stayed on the farm instead of moving to town and opening the store, and so on. Those ideas are fine. And Tomasi can use those ideas and build on them without having to copy the tone and characterization that made SO itself so f**king terrible.