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As far as your issue goes, why not just fix all the query strings with a couple lines of mod_rewrite and not worry about where they came from?
There's no way it can have the opposite effect if it's implemented correctly, because the pages should not ever be accessed, and if they are then you're simply noindexing duplicates of the canonical version.
If they don't ignore the parameter for some reason, then both will be found and have the same effect as the "ignore" should.
... and that's exactly what I meant about conflating two different aspects of parameter handling.