Getting rid of Windows Messenger is a must. It's just a pain and not needed for the average home user. You can remove it without affecting MSN Messenger.
Two methods:
1. Download and run Shoot the Messenger
http://grc.com/stm/shootthemessenger.htm(This will disable the messenger service.)
2. Remove it through Control Panel, Add & Remove Programs. Go to the Windows Components and scroll down to the bottom of the list. Remove the tick from the box next to Windows Messenger. (This is my preferred method - get rid of it altogether.)
Dave