With proper preparation I can see Urahara winning, just like Aizen did—but even then it's sketchy because Aizen had years of preparation, no ethics limiting his research, and he relied on Yamamoto sacrificing himself to prevent the destruction of Fake Karakura Town.
But the difference in raw power is just too great for Urahara to be able to defeat him without a prepared strategy and contingency plans.
But Yamamoto did survive the release of the fire when he threw himself over Wonderweiss' body—after he had sealed the flames—to absorb the explosion which would've reduced the entire town to ash.
I'm not saying that it couldn't kill him, if he used to full effect. What I'm saying is that he doesn't necessarily have to use it to its full effect, in which case it won't kill him. And I don't think he'd have to use it to the same effect on Urahara as he would had on Aizen.