Just found a useful FAQ about exclude some httpmodule inheritance in ASP.NET web application(from parent ASP.NET application). It demonstrate two approaches:

 1. Modify the parent web.config file to disable child app inheritance(element based)

 2. Explicitlly remove certain httpmodule in child web app web.config file.

#How to disable web.config Inheritance for Child Applications in Subfolders in ASP.NET?
http://www.aspdotnetfaq.com/Faq/how-to-disable-web-config-inheritance-for-child-applications-in-subfolders-in-asp-net.aspx