Will I be sinful if employees use the payroll program—which I programmed—in an Islamic Murabaha transaction, knowing that I cannot stop them from using the program?

There is no objection to Murabaha selling if it adheres to Sharia (definition) guidelines. There is no objection to your programming work, even if it involved a salary certificate for the employee. If the employee uses it for an unlawful purpose, such as borrowing with interest (riba), the sin is upon them. Since you completed the programming before banks began using Murabaha, there is no sin upon you, because a salary certificate is used for many purposes, and its use is not exclusively for unlawful acts.