IE is made by Microsoft yes but you use Windows, also made by Microsoft...
Another alternative for stripping down XP/2000 is
xplite and its Win2k version (you don't state your Windows version hence YMMV).
Theres also an ActiveX plugin for Mozilla (Seamonkey and FF). That _may_ work w/Windows Update. However if it does not you can grab patches from Microsoft.com anyway, you do NOT need Windows Update to grab patches.
Also, you can use your prefered browser/frontend, set it as default browser, and only use IE for Windows Update. You can even tweak your IE settings to only allow _that_ website (See: Config Screen -> Internet Options). Theres even an extension for FF to open Windows Update. It opens IE then, to Windowsupdate.com, and voila.
Avant Browser uses the IE rendering engine. Same as MyIE2 / Maxton. Just a frontend w/additional features.
I suggest to use the browser/frontend which you prefer (whatever it may be), make sure you secure it and futhermore keep a note on its patches / vulnerabilities. Run a virusscanner and/or registry-watcher and/or anti-spyware program (realtime or not) and you are generally secure. IE, FF and the like can also be tweaked to secure settings i believe XP/SP2 and Win2k3/SP1 come w/advanced security features (for IE) enabled. Futhermore just use IE for Windows Update (easy; easier than manual install for the avg home user) and hence don't uninstall IE either the 'unlink' way or the 'hard' ("lite") way. Its not worth the hassle. Just change your default browser, in XP/SP1 and higher: Start -> All Programs -> Change Default Programs -> Browser -> Custom -> Select your prefered browser (you may have to install yours first).