McAfee would never block Windows Updates provided you are trying to install them using Windows/Microsoft Update. Even if they were individually downloaded all it may do is popup a check box but still wouldn't block them. Something else is at work there, Have you had any other strange happenings?
Also is this Windows 7 SP1 and do you have, even if you never use it, IE11 installed? (The reason I ask is because McAfee UI uses it).
The only time you need to disable the antivirus is when installing Service Packs and that is a very rare occasion.