Use Sandboxie and configure it. Don't know about anti-virus providers that protect the MBR, but I'm sure most do anyway. There is software to back up the MBR though...
If you wanna dork this out check out untangle. It's a HIPS firewall and anti-virus solution for your network. All you need is a cheap computer or server and install. They list known working computers and servers. https://www.untangle.com/
If you ever hose it, you can overwrite the MBR and write a new one / denote the proper bootable partition with something like gparted as well... though this would not guarantee the security of the bootloader on that partition.
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