Uh, excuse me fallible but if you wanted a clear answer you should have phrased a clear question that even the slowest turtle in the tank could have understood. Here's what I think you've asked...

Do we have a list of words that don't mean what their etymologies suggest?

The answer to this is yes. All words are in a state of transition and the meanings of all words differ in the absolute with each usage. But the answer is also no because all words have deviated from their origins and no lists of all words exist.
So you must mean something else.

Frankly, I don't really give a rat's ass what words mean - well, more like I don't care to define the words myself. I mostly just infer meaning from other people's usages.

I see.

What I'd like to know is:
What are some examples of (other) words whose meanings don't jibe with their etymologies. I'm particularly interested in words whose meanings actually contradict their etymologies, but a stark contrast would be sufficient.

This seems pretty clear. You are asking for a list of words that at one point in their careers meant almost the opposite of what they mean to most people today.

Yes. I remember tsuwm had such a list. It was a small list and atheist, theist, agnostic, and gnostic were not on it.

Anyway Fallible, you didn't ask, but I think your definitions of "atheist and agnostic" come closer to being widely understood than those of your anonymous correspondent. Have a nice trip.