When you sign in to Windows Live Messenger, also called MSN Messenger, for the first time, you are given the option of connecting your Facebook account to the program. If you did this but later changed your mind, you can easily unlink your Facebook account from your Windows Live account within the Facebook privacy menu. You can also do this through the Messenger interface.
Log in to Facebook and click on "Account." Click on "Privacy Settings."
Click on "Edit Your Settings" beneath "Apps and Websites."
Click on "Edit" next to "Apps You Use." Click on the "x" next to "Windows Live Messenger."
Click on "Remove."
You can also unlink the messenger from Facebook by click on "Add>Manage Your Services" in the bottom right corner of the messenger interface. Click "Remove" next to "Facebook."