Actually the problem is that whenever you switch back to Visual mode, whatever code WordPress doesn't like is removed or changed. It is easily one of the most annoying features of WordPress if you like to embed videos, or really anything that uses anything but the most basic HTML. At the very least, it should have an option to turn this feature off, but it doesn't.
So I am totally with you, for a site that claims "Code is Poetry", this sort of code Nazism is completely ridiculous, and saying "Well just don't use Visual mode" is not an acceptable alternative.
and @Darrell: This problem has absolutely NOTHING to do with what theme you are using, what CSS is in that theme, or TinyMCE.