I beg your pardon in advance for the complicated answer, but I don't quite grasp what you want to do (or better: why).
I think that you are looking for the
FDISK /CMBR command. There are also utilities that perform the same task, e.g. Paragon Partition Magic, or Boot/Partition Editor.
What you want to do is to rewrite the MBR and set the D: partition to non-system (not active, not bootable, no B flag, etc.).
Note that FDISK /CMBR should act only on a non system disk; many boot loaders install code that is needed afterwards to "see" the disk with the correct format or geometry; replacing them with a stock loader (which is what /CMBR does) can then render the disk unaccessible until the previous code is restored.
If you need to make the disk non-bootable because it interferes on the boot sequence or something (and displays a "NTLDR not found" error instead of booting, say), a better choice would be to modify the BIOS parameters for boot device order or using a FDISK-like utility to mark all partitions on that drive as non-system. In a pinch, swapping two hard disks ought to achieve the same result.
Otherwise, there are "selective boot loaders" (e.g. GRUB) that may help you implement a flexible booting option (e.g. booting Linux, or Windows, or another Windows from a startup menu screen).