Have you checked the pads yourself? I'd whip a wheel off and have a good look.
Did the front sensor go off, or the rear? Which one wouldn't reset? They are quite separate and should show separately on the dash, and be reset separately.
It is true that they can measure the outer pad thickness without removing the wheels - they insert a special tool (though the back end of a vernier caliper will also suffice) into the wheel and can check the outer pad thickness as there is a hole in the pad to the disc. It is better than a visual check that is not really accurate with the wheel on. You can't check the inner pad the same way with the car on the ground, but maybe possible with it in the air, not sure. The sensor is on the inner pad.
It is usual for the pads to wear evenly, so its quite normal for them to only check the outer pads. I'd be wondering why on earth they are not wearing evenly - caliper problem? incorrectly fitted? What was their explanation? How much is left on the outer pad?
EDIT - why the heck couldn't kwikfit reset the indicator? Don't they use (read) the correct service procedure!?!? If my local village garage can, it shouldn't be beyond kwikfit.