I think an important part of the argument is the context it's being used in. In Damore's essay, it was used as a counter to the idea that anything less than a 50/50 gender ratio was obviously a result of bias and discrimination. In that context, I think highlighting the possibility of other explanations might be appropriate. If he was instead arguing that Google should stop trying to hire women because they might be less capable, that would be a clear indication of bigotry.

I have a lot of problems with how the issue was raised by Damore and I think his firing was appropriate, but I also agree that his essay has been wildly mischaracterized by the media.