This issue wasn't a huge problem for me in the past (I originally posted all blog posts using the HTML editor, though I recently began using the RTE - primarily because I didn't often need to add raw HTML by hand for writing blog posts).
However, I'm in the process of converting about 100 of my site's (external-to-WordPress) static PHP pages to WordPress pages, and ran smack into this issue. It was, indeed, quite a pain.
I would be happy just having a configuration option to disable the RTE from modifying HTML input using the HTML editor.
Perhaps a plugin is the way to go?