Unfortunately their answer was to make my primary experience (the pc) ugly so that they can try to compete for my secondary experience (phone)

Start> type - is a search functionality. Typing "power" is likely sufficient to identify your "Microsoft Office PowerPoint Viewer 2003" application.

You've explained why everyone had it installed, but not why everyone used it. Their bundling ensured that IE was installed on every computer, but it didn't prevent the user from simply installing and using an alternative. The quality of IE4 did.

or turn off the feature that they are currently not using.

As a CA, MS will revoke the certificate. This will not help already infected machines, but will instantly protect any machines not already infected by removing the certification of the malware. Think SSL when a site has been compromised, and remember that if the scheme fails we are simply back where we started.

Even if the key is stolen as you predict, then the net result is that any program can install itself as part of the boot process, and we've done nothing but return to our current state. If however, the key is kept protected or some malware fails to use it, then we have a more secure boot process. Note that I've said more secure, and not secure.