I can't say for sure, I'm just an avast user, but even if it did protect the master boot record, I don't believe it would stop it from being edited or deleted. As confirmed by Igor.
I'm not sure why you would want to get rid of the MBR as without it your computer is stuffed (sorry about the technical terms). I have Partition Magic V 8.0 and I can't recall any time that I needed to kill the MBR.