Joel Reyes has been doing Visual Studio Tools for Office (VSTO) presentations at our dev conferences and as webcasts.  During our conference in Juneau, AK, someone in the audience asked him something to the effect of:

"The new Office 2007 file formats are just compressed files.  Why can't VSTO based documents just package all of the assemblies necessary for the solution inside of the file?"

Joel explained that embedding the assemblies inside of the document opens up a number of security risks.  Therefore, direct embedding is not an option.

When I introduced myself I promised to follow up with anyone who had follow on questions.  Of course said customer took me up on the offer:).  As promised, here are the MSDN Library links for further exploration:

Visual Studio Tools for Office - http://msdn2.microsoft.com/en-us/library/d2tx7z6d(VS.90).aspx

Deploying Office Solutions - http://msdn2.microsoft.com/en-us/library/bb157879(VS.90).aspx

Security in Office Solutions - http://msdn2.microsoft.com/en-us/library/bb386278(VS.90).aspx

-Marc