I imagine the commenter is concerned about the colonial/bigoted connotations that word carries when applied to people groups.

Pygmys are a subset of a species whose physical attributes are smaller than the main species. Applying that to people is obviously... Problematic at best.

I don't see how reusing the word, given its original use in biology, is directly causing harm. If anything I think it's a clever and decent reclaimation of the word.