Although you easily sign scripts that are standalone I don't think this helps when they are run with IE as a host. The alternative is to put your site into "Trusted Sites" or "Local Intranet" security zone. You users will have to do this unless you can add it via a login script or similar, I don't know if this is possible in your case.
These two zones normally have lower security settings so your script should run. One more thing to be aware of is that you cannot use the"Wscript" object directly if the code is run in IE. This means things like "Wscript.sleep" etc. will need to be re-written.

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Joe