Is it permissible for an employee to take free samples from the pharmacy without the employer's knowledge, even though the supplying company allows it, and with the intention that the employer is stingy and might forbid it?

What appears to be the case is that the samples are given to the pharmacy itself. Therefore, the employees are not permitted to take anything from them except with the permission of the pharmacy owner, because he is the proprietor. This differs from a situation where the samples are given to the employees in their personal capacity, in which case the permission of the pharmacy owner is not required. Rather, it is sufficient that the condition of the granting entity—namely, the company providing the samples—is met, so long as it has no objection to their benefiting from them as employees and pharmacists.