Does it just make noise when you pull the brake, or all the time? If its just when you brake, maybe you could have them put some sort of plastic sheath over the cable. Or have them try reaming out the little holes that the cable runs through, slightly. Or you could check out the Jagwire Pro series brake cables and housing- those kits have sheathing and ferrules that might help with friction where the cables enter/exit the frame.

I have an internally routed bike- my brake cable taps the frame when I'm on rough roads. Gotta remind myself to put some cable donuts on the brake cable next time I have it apart. This kind of stuff doesn't generally have an official fix, its just about getting creative and solving the problem.