What should the pharmacist do with the money he received for leasing his pharmacy license to a non-pharmacist, after he learned that this is impermissible according to Sharia? Should he return the money to the person, or pay khums on it, or donate all of it as charity?

It is not permissible to lease a pharmacy license, and its rental fee must be spent on charitable causes and not returned to the lessee. However, it is permissible for one who was unaware of the impermissibility to benefit from that fee, though it is still more preferable to spend it on charitable causes.