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Although I can't test it right now I am pretty sure that this works:
IF the manifest for a DLL is external it will usually be ignored when the DLL is loaded via LoadLibrary (according to MSDN). IF the manifest is embedded into the DLL it is usually honored.
LoadLibrary
Embed the manifest into the ASP.NET application (i.e. code-behind DLL) - for some ways on how to do this see here and here and here.
UPDATE - as per comments:
The above is a workaround as there is no general way to do this (isolation), at least the ASP.NET creators haven't intended this to be possible - for example the above workaround won't work in cases where the application does not compile to a DLL...