I did a little digging around and have concluded the presence of IE should
have no effect on Windows' Automatic Updating, as long as it is enabled. I don't use the feature and prefer to manually update instead... the idea of Windows doing things like that by itself gives me the creeps.
The only downside is you won't be able to connect to the Microsoft site that scans your system and generates a list of updates and some optional hardware drivers available. You still have an ability to manually update via their Downloads Center, but without intimate knowledge of what you need and already have... it might be a migraine-producing affair.
Anyway, for more info try accessing the below link using FireFox (or any other non-IE browser) and read the nifty message scrawled there gently chiding you on your selection of browser (LOL!):