So true! There is a time and place to Write Well, Write Correctly. :-) But those situations are becoming more rare. The thinking that "you need to know the rules, and break them with intent and considered purpose." ... like my refusal to put anything inside quotation marks that are not in the original quote. Example: "Yes, I feel similarly" he said. as opposed to "Yes, I feel similarly," he said. I want my students to, at least, be aware of those little things even if they don't subscribe.
Are you 100% sure that the comma after yes was in the original quote? If you are, how do you know that the second comma was not? Of course, do whatever you like. Generally we separate the speaker from the spoken words with a comma. That is why we say, He said, "Yes, I feel similarly." In that case, though, the comma is outside of the quotation marks and, thus, not breaking your self-imposed rule.