Thanks Limey. I've decided to just put the new EBC pads on and run it like it is, and keep an eye on the pad wear. If the braking feels compromised after the break in period, or it's too noisy, I'll just replace the rotor and go back to OEM pads. If all is good, I'll probably run the EBC pads until they wear out, and then replace the pads and rotor. I don't know how long the EBC pads last, but I was getting 15,000 miles or so out of a set of OEM pads. If I even get half that out of the EBC's, then the rotor will have almost 40,000 miles on it and will probably be due for replacement anyway.
I definitely now believe the reports that the Super Teneres are really hard on the rear brakes. My front brakes have just shy of 14,000 miles on them, and they look great. I managed to wear the rear pads down to the metal in just 15000 miles. The previous set had 15,000 miles on them when I changed them, and they were pretty worn out too (but not as bad as the current set). I suppose that's a byproduct of the linked brake system. Lesson learned, though; I'll definitely keep a better eye on them in the future.