Does a Macbook Pro have 1 or 2 Hard Disk Controllers?
It has two and yes, you can make the controller that connects to the SuperDrive spot the primary controller and run your MacBook Pro exclusively off a drive attached to this controller.

I'm writing this from a MacBook Pro that has an SSD installed into the SuperDrive spot using an OWC DataDoubler bracket. This is the primary drive in my machine and the mechanical drive has come and gone from the machine without any issues. The machine still booted, ran from my SSD in the SuperDrive spot.