I have some additional information regarding my post the detailed the deleing of application sub-directories and the resulting AppDomain restart. If you delete a subdirectory (containing ASPX pages, etc) using the Windows Explorer, the only file change notification ASP.NET receives from the file system is that the subdirectory was removed. We do not receive any notifications for the files in that subdirectory. The file system guys say this is because the Windows shell moves the subdirectory to the recycle bin, and the file system does not treat this as a change to the files.
In v1.1, we would continue to serve the content in that subdirectory. As a bug fix in v2.0, we decided to unload the AppDomain to ensure that we do not serve the "deleted" content.
Aside from not deleting the directory, there is no workaround and at this time we are not working on a fix.