Is it permissible for a pharmacist to continue with a work arrangement that does not take up all of her time, while receiving a full salary, and then give a portion of it to Allah to purify the remainder? If so, what is the amount of this portion? And what is the ruling concerning the salaries she has received previously?

If the employment contract requires your daily presence at the workplace, you must fulfill this obligation whether there is work or not. Otherwise, you do not deserve the wage for the period you failed to honor this right. The original principle is that this amount should be returned to the employer. If that is not possible, it should be spent on public welfare or given to the poor and needy, unless the employer absolves you. You should repent for this shortcoming in the future.