After some digging around, it appears that project files for C# are stored in \program files\microsoft visual studio 9.0\common7\ide\projecttemplatescache\csharp\windows\1033. By adding <UseVSHostingProcess>false</UseVSHostingProcess> to the correct sections (there are separate sections for Debug and Release configurations) of the relevant templates, you can turn off the hosting process for all future projects of the selected types.
You should be able to handle the PDB issue in a similar way, but as I said I don’t recommend turning those off, so I’ll leave it as an exercise 🙂
This applies to VS2008, but my guess is that other editions have a similar scheme. In fact, VS2010 uses the same approach, but obviously the version number in the directory is 10.0 instead of 9.0.