There is an attribute that you can use in the root web.config file to cause it not to have its contents become inherited by child applications.
inheritInChildApplications
Blog about inheritInChildApplications
MSDN article on ASP.NET Configuration File Hierarcy and Inheritance
Put the part of the config that is not for inheritance inside
<location inheritInChildApplications="false">
<NotInheritedConfigPart/>
</location>
Config sections seem to be impossible to not inherit, but other parts of configuration can be “commented” out like this and don’t get inherited.