Michelangelo and similar viruses only activate when you boot from the disk it's on. Insert a disk with Michelangelo in a running system, then format the disk (make sure you overwrite the boot sector), all OK.
The operating systems of the time didn't have any autoplay functionality that could be exploited by viruses. I guess in theory viruses could have exploited things like buffer overflows in the OS code that reads the file allocation table or directories, but I've never heard of such a thing, and Michelangelo and similar boot viruses certainly were not that advanced.