Not to be a grammar nazi, but I think you mean 'flesh'. "Flushing" something out sounds toilet-related. Gross.
And "flush" is perfectly correct. Used transitively, it means "to expose or chase from a place of concealment." Example: "the hunters used dogs to flush their game from the bushes."
In figurative language, "flush" is a good choice when you're talking about stripping away extraneous information. "Flesh" is used when you're proposing to add more information, as in putting flesh onto bones.
I should add that I'm only addressing your claim that "flush" is inherently scatalogical, not whether the original use was valid.