This is the wrong shilah.
The shilah should be, is it mutar to work for an organization that violates explicit Torah commandments?
The Torah explicitly requires that employees be paid on time. How can a yeshiva that violates this commandment be considered Orthodox? We would never countenance a yeshiva serving treif food in order to save money. Yet Chazal tell us that financial transgressions are worse than arayot!