I feel your pain. And this is my point to the obstructionists who won’t question a retarded feature and would rather tell you to spend your days developing work-arounds rather than address the apparent problem: TinyMCE can’t validate its own code. It’s afraid of div tags blowing up the site or something. We still should be allowed to turn off its stripping features.
What I did was install two plugins – TinyMCE Valid Elements and Ultimate TinyMCE. The first is probably all you need but better safe than sorry. Just download and install from the plugins page.
Then you’ll find TinyMCE Valid Elements options, not under the plugin or settings, where it should be, but under TOOLS. Add an element like “A” for a link, then you can add attributes. Then the code won’t be stripped. Presumably. I’ve still had problems, but I’m told the “documentation” will help us.