"at will" has nothing to do with it. It's related to exempt status.
Exempt (salaried): This exemption is meant to exempt individual employees rather than entire classes of employees.
Pre-1998 regulations provide that certain administrative, executive, or professional employees are exempt from coverage of the overtime laws (i.e., they are not entitled to overtime pay), provided that at least 50% of their working time was spent performing work which is primarily intellectual, managerial or creative, and requires the exercise of discretion and independent judgment. Under this test, many supervisors and managers were exempt from overtime.
[as you can see this would not apply to programmers and others doing similar work, hence the lawsuit]