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If you insist, look into the Javascript methods of focus(); basically if your pop-up is open and they return to the main window, you force focus to the pop up.
Why do you actually need to "disable" the parent window?
You want to prevent them clicking on the main window or?
Do you just need to force the pop up window in focus?
If you can provide a little bit more info, maybe we can think of something :)
But, like @rocknbil said, there are methods that have the effect. You could redirect the user to another page or a blank page (about:blank) after clicking on your link. Try this:
<a href="about:blank" onClick="**insert your JavaScript window-opening code here**">Start the App!</a> ...but still, why not just load the app in the current window? The only issue I can see is wanting to disable the back/forward buttons but technically savvy users can still do this using key commands. If this is the case re-write your code so there would be no issue if users *did* do this. Another solution to this is invoking IE by command line to disable the toolbars. As much as I hate IE, if you must use it, then this is an option.
Well, I've rambled too long. Hope I've helped.