Jeg har ikke prøvet det, men et bud kunne være at skrive til web.config programmatisk. Det er nok f.eks. bare at sætte LastWriteTime, så du undgår at skrive til indholdet.
Jvf. MSDN
http://msdn.microsoft.com/en-us/library/ms178473.aspx:Application Restarts
Modifying the source code of your Web application will cause ASP.NET to recompile source files into assemblies. When you modify the top-level items in your application, all other assemblies in the application that reference the top-level assemblies are recompiled as well.
In addition, modifying, adding, or deleting certain types of files within the application's known folders will cause the application to restart. The following actions will cause an application restart:
Adding, modifying, or deleting assemblies from the application's Bin folder.
Adding, modifying, or deleting localization resources from the App_GlobalResources or App_LocalResources folders.
Adding, modifying, or deleting the application's Global.asax file.
Adding, modifying, or deleting source code files in the App_Code directory.
Adding, modifying, or deleting Profile configuration.
Adding, modifying, or deleting Web service references in the App_WebReferences directory.
Adding, modifying, or deleting the application's Web.config file.
When an application restart is required, ASP.NET will serve all pending requests from the existing application domain and the old assemblies before restarting the application domain and loading the new assemblies.