Is "Darwinist" A Loaded Term?

A reader writes:

Full disclosure: I'm an atheist -- as in, not a theist -- so take this as you will. 

I enjoy reading your discussions and contretemps with readers about religion. As an atheist I'm in a minority, I know it, and while I've got my issues with religion in the main I'm also not blind to the fact that many religious people and institutions (Western and non-Western) have served humanity well.  I'm not going to bash here.  But I am going to call you out on "The Darwinist."

Please.

I've only ever known that phrase as a disparaging appellation used by religious fundamentalists to attack those who agree with the theory of Natural Selection. This is a tired ad hominem meant to mark "non-believers" as idolaters who worship Charles Darwin, a mere man, and his heretical idea, a mere theory.  I'm not suggesting that you or your readers are dishonest or intentionally arguing dishonestly, but this is loaded Scopes Monkey Trial language that tilts the conversation unfairly.

It's hard to take a passage like this seriously when it's used to argue against "The Darwinist:"

"So to argue over the precise timing of Adam and Eve "eating an apple," as your one correspondent did, is nothing short of bizarre -- its genuinely a world of discourse thousands of years out of date. You know this, of course. But its striking how many of your presumably secular or at agnostic correspondents imagine a religious response to evil and suffering only through the terms set by fundamentalists. They counter a stilted argument proffered by fundamentalist theology then go on as if their work is done. This not only is pretty cheap intellectually, but incredibly impoverishing for our public discourse. The best word for it, I think, is ignorant. "

"The Darwinist" is from a discourse a hundred years out of date, a term set by fundamentalists, and also pretty cheap intellectually, as is "The Jew", "The Homosexual", "The Negro", and so on.

Let's play fair.

I'm sorry but this is so touchy it's pathetic. I'm a Darwinist, for Pete's sake, in as much as I find that great man's genius to be a highpoint of human civilization and insight. No pejorative was implied or asserted. Yes, it's shorthand, but shorthand is not the same as terms such as "the negro" when deployed in a disparaging sense. (And I use the word "homosexual" myself as a neutral term.) More to the point, my reader used several terms for those with whom he disagrees: "secular or agnostic", "non-theist,"  "scientist", "atheist". The word "Darwinist" was used once in a phrase I thought provocative enough to make the title.

Good Lord, the touchiness on this subject. Get over yourself.