Is it permissible for an employee to prepare a general administrative program for a massive food company that includes a section for selling alcoholic beverages, knowing that he will soon be asked to present his accomplishments to the company's executives?

If the program is suitable for permissible and other uses, and you do not know its field of use, there is no harm in preparing it. However, if you know that among its uses is the sale of alcoholic beverages, then it is not permissible for you to prepare it, due to the assistance it provides in marketing prohibited items, and the means share the rulings of their ends.