I have an ASP.NET MVC 2 application.
None of these answers are sufficient in my mind. This does seem to be a genuine bug. I will update this response if I ever find a non-hack solution, or Microsoft fixes the bug.
Update:
Doesn't seem promising. https://connect.microsoft.com/VisualStudio/feedback/details/731303/publish-web-feature-not-including-all-dlls