I've already got a single disc set up on my DD bike.
With a m/cyl designed for 2 discs, you're pumping twice the volume of hyd fluid that you now need, in other words the pads move twice as far for a given lever movement than they did with two calipers. So you end up with roughly half the lever movement for a given pad movement, which means much less ability to modulate your braking unless you switch to a m/c that pumps less fluid, like a 16x18. I suggest you do that.
You do only have half the braking (limited by the amount of kinetic energy the disc can radiate as heat), but when I worked out the maths it showed that a DD bike needs to dissipate almost exactly half the KE of a 996 (slightly less weight, much slower), so I figured that the exact same disc/caliper/pad set up I have on the 996 ought to work fine on one side of the DD. And except for outbrraking myself a few times at Snetterton , it does.
