There really isn't any human disease that they are going to pass on to your reptiles, zoonotic disease from mammals to reptiles are rare. In that respect the clerk is more a danger to *you* than your snake.
As far as picking up another reptile and then touching a feeder the biggest risk there would be mites. For the most part bacteria and virus need very special conditions to live in, even if you did manage to transfer a bacteria or virus onto a rat it would then need to survive the elements and then survive the digestive system of the snake and still be present in enough quantity and in the right vector to infect your animal *then* it would have to survive your snake's own immune system. A reptile can pass a disease to another reptile fairly easily, but if you add two different mammals into the cycle and only casual contact as a method of transference the chances of the bacteria/virus getting a foot hold is low.
All in all unless the store is disgusting and just full of mites and risk is very low.
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