There is no way I know of to restrict your operating system to access all the components connected to your computer. Of course you can dual-boot between different operating systems, even if they are the same - say 2x win7 - but the one OS will still have - at least basic - access to the other drive. (if you take security measurements, the malware has to be pretty advanced to access the other drive though, most malware will not be able to do so, but it is still not impossible)
If you want to seperate the physical hardware layer from the logical layer your operating system provides to your applications (and malware) you would have to put a layer in between the operating system and the hardware. The only solution I see here is to run a virtual machine.
The other solution would be to physically change the harddrives, there are several solutions available that support changing drives via front panels.
But, there is malware that can write itself to the boot sector or even to the BIOS' flash, against those baddies changing drives or encrypting them (as recommended by ekaj) will not help. An encrypted drive aditionally only makes the files on it unreadable, but the drive can still be accessed by the malware and get corrupted. I still highly recommend a virtual machine, although there is malware out that is able to escape such secure enviroments.