You are not going to have much success with this.
The security architecture of web browsers is designed to prevent websites from running programs on local machines. With special exceptions for cases like PDF files.
Perhaps you should consider another architecture. Opening Word documents in InDesign is already an abnormal workflow.
Let me clarify this a bit, i already have a method of getting the documents and script onto the local machine and of launching InDesign from a web browser, i'm wondering if a script can be passed in to the launch command as an argument or if i need to put it in the specific startup folder then have it deleted when done.
Mac or Windows?
And for that matter: CS5?
Hopefully someone else can help you then. On a Mac you could certainly have AppleScript launch InDesign and then have it run an existing script, or open documents on its own. I imagine you can do something with VBScript.
This assumes, of course, that you can run something other than InDesign with your browser framework.