The employee's religion is a Pentecostal of Christian faith that requires women to wear only skirts or dresses. She brought this up at her interview for a BK cashier position, and the interviewer assured her it was not a problem. She got the job, but when she showed up to work in a skirt she was sent home.
Generally, employers are required to reasonably accommodate the sincerely held religious beliefs of their employees unless it would impose an undue hardship. Courts have allowed uniform requirements to trump religious garments in limited circumstances. For example, a prison can ban religious headscarves to prevent smuggling of weapons and contraband, and to prevent the scarves from being used to strangle people.
I doubt Burger King has such concerns. Although I guess it's possible that loose clothing presents some hazard around the kitchen. If the manager is just worried that the skirts clash with the BK unis - well, that sounds like an uphill battle to me.
HT: Prof. Volokh and his Conspiracy (he has additional analysis and citations).