We use a web single sign on product Siteminder to protect any web application in our enterprise that requires a user to log in with their AD credentials. We are looking to protect the web reports from our SQL 2008 reporting services with Siteminder. Usually, we install an ISAPI Filter in IIS that intercepts the web request and redirects them to our login server for authentication. However, SQL 2008 doesn't rely on IIS anymore. Does anyone have any experience with this?

You can use a custom extension for ssrs. Mainly a security extension. This will however involve some programming, unless you can find an extension that works already. http://msdn.microsoft.com/en-us/library/ms152934.aspx