Again, even older thread now, but we got around this problem differently again!
Instead of copying the DLLs into the bin folder, we amended the web.config in the virtual directory to remove the referenced files.
E.g.
<httpModules>
<remove name="XHtmlModule" />
</httpModules>
Version was 3.0.
This works because of the way .net manages the inheritance of the web.config files.
Hope that helps,
James
http://www.distinctionhq.com