The law absolutely does prohibit having different policies when those policies have a direct impact on a person’s status as a protected class or on protected federal leave. For example, you cannot say “Department A will be granted 12 weeks of unpaid medical leave if needed, but Department B can only have 6 weeks of unpaid medical leave because we’ll be short-staffed.”

The EEOC routinely investigates disparate impact claims, which are when policies which look neutral on the surface impact a protected class. For example, a company that has a policy of only providing 10 sick leave days and not allowing employees to take sick leave for a full year? That disparately impacts pregnant women (See Abraham v. Graphic Arts. Int'l. Union).

For Mary to make her case, all she has to do is identify an employee who was similar in their ability or inability to work due to an impairment and who was provided with the accommodation that she is seeking. Case in point: OP’s wife.