I asked this question this morning. Essentially there's an IE hack in the Silverlight.js file that breaks in...IE9.
The response I got was to get rid of the file altogether which, to my surprise, seemed to work after preliminary testing.
So does this file actually serve a purpose?
I believe this was included as a way to launch Silverlight on browsers with an advanced "install" experience, or to show alternative HTML when Silverlight was not installed.
http://archive.msdn.microsoft.com/silverlightjs
http://msdn.microsoft.com/en-us/library/cc265155(vs.95).aspx