Managed to come up with only one work-around, that'll still allow the file change notifier to monitor web.config and bin directory, and it's not very pretty, but it seems to work:
private void SafelyDeleteFolder(string folder, bool recursive)
{
//FIX disable AppDomain restart when deleting subdirectory
//This code will turn off monitoring from the root website directory.
//Monitoring of Bin, App_Themes and other folders will still be operational, so updated DLLs will still auto deploy.
System.Reflection.PropertyInfo p = typeof(HttpRuntime).GetProperty("FileChangesMonitor", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Public | System.Reflection.BindingFlags.Static);
object o = p.GetValue(null, null);
System.Reflection.FieldInfo f = o.GetType().GetField("_dirMonSubdirs", System.Reflection.BindingFlags.Instance | System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.IgnoreCase);
object monitor = f.GetValue(o);
System.Reflection.MethodInfo m = monitor.GetType().GetMethod("StopMonitoring", System.Reflection.BindingFlags.Instance | System.Reflection.BindingFlags.NonPublic);
m.Invoke(monitor, new object[] { });
System.IO.Directory.Delete(folder, recursive);
}
{
//FIX disable AppDomain restart when deleting subdirectory
//This code will turn off monitoring from the root website directory.
//Monitoring of Bin, App_Themes and other folders will still be operational, so updated DLLs will still auto deploy.
System.Reflection.PropertyInfo p = typeof(HttpRuntime).GetProperty("FileChangesMonitor", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Public | System.Reflection.BindingFlags.Static);
object o = p.GetValue(null, null);
System.Reflection.FieldInfo f = o.GetType().GetField("_dirMonSubdirs", System.Reflection.BindingFlags.Instance | System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.IgnoreCase);
object monitor = f.GetValue(o);
System.Reflection.MethodInfo m = monitor.GetType().GetMethod("StopMonitoring", System.Reflection.BindingFlags.Instance | System.Reflection.BindingFlags.NonPublic);
m.Invoke(monitor, new object[] { });
System.IO.Directory.Delete(folder, recursive);
}