Outlook will try numerous methods of starting it up.
If it can't find it by one it will carry on through it's list of ways so if you don't kill them all you can end up waiting a very long time for outlook to start.
I'm not aware of how to disable messenger in that way although there are plenty of methods of uninstalling it.
If anywhere has the answer it's likely to be
TweakXP.
This article assumes you've allready removed messenger but, from looking at it, it's possible it may also disable the startup call. It's worth a try anyway.