Hi!
I think, it is very good idea to develop( or buy from others and put in CIS 
) Master Boot Record Agent
Agent should be able
- to save MBR / load saved
- reset to default settings
- alert to user, if some program want to make a change to MBR
- on every day base/ windows restart shall be automatic verification of MBR .Is it ok, or it was changed…
And if MBR was changed- only then will be an alert