Abba_S: Your example of a worker is highly dependent on the job. The rule is “reasonable accommodation”. So in your case, let’s say someone was working on Sundays, but not on Saturdays, because he’s Shomer Shabbos. Now, the store became a lot busier on Saturdays, and less busy on Sundays, so the owner decides to cut staff on Sundays and increase staff on Saturdays. In such a scenario, the worker wouldn’t have a case, because the business need is to work on Saturday. There isn’t a reasonable accommodation.
In this case, if the money isn’t there, they need to cut services. The religious belief for separate busing isn’t a priority for them – separation of church and state and all that. They can try for a reasonable accommodation, but they still need to work within the budget that they have.