Superficially the one pad we can see looks no more than 1/3 to 1/2 worn, but the surface condition is not very clear, nor are any other pads shown. Rear pads cannot be seen properly with the wheels in place. It is not a good idea to rely solely on the visible tell tale since one pad of a pair could be almost non existent. With the warning light on, although one could wind the caliper adjustment off for a better view, they probably pulled the wheels off . Since this is not necessarily as easy as it sounds - they stick fast on the hub - having spent that time getting the wheels off they probably decided to reline anyway.
If they had told you that having taken the wheels off for a better look and decided to leave alone would you have quibbled about paying the labour involved? 100,000km sounds reasonable to expect the pads to be ready to be replaced.
It seems a little strange that having found a problem with the warning light circuit the vehicle was returned, unless of course they were pressured to do so.