James,
There is much in positivism that is useful. But I think that the view that positivism is an objective scientific stance is a bit off the mark. I have always viewed positivism as a subjectivist philosophy of science. It is especially to be criticized for its theory of causality, which is decidedly Humean, positing that causal relations are mental events, reducing cause to constant conjunction. Positivism suffers from misplaced concreteness, reifying space-time points and other such imaginary entities and deny the reality of the structure of the world that make rational comprehension of the world possible.
Positivism as practiced in the social sciences is said to be the model developed from the natural science, but this is not true. Natural science actually proceeds differently. I think positivism has generally been replaced as a philosophical stance throughout science by scientific materialism.
I do agree with you, though, that, like criticisms of structural-functionalism, much of the popular discourse on positivism constitutes a strawman. Most people who criticized positivism do not do so from their own examination of the position(s).
Andy
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