Running Knoppix from CD should not affect your HD in any way. By default HD partitns are detected but not mounted. When mounted manually by the user the default mount is read only. It will read NTFS partitons and has the capability for 'captive NTFS' to write to the HD if desired (user must manually mount the drive then change it to read write first).
Running from CD it does not do anything to your boot sector.