Should religious businesses whose owners are opposed to war be able to deny Service-members their Veteran's rights?

I am writing (edit: already wrote) a paper on the Hobby Lobby decision, and I know that many RP members are deeply religious. For obvious reasons, almost no RP members are conscientious objectors (i.e. opposed to all war and supporting it in any form; pacifists are one example). Do you think a religious business should be able to deny a Reservist to return to his job after a deployment? This is a hypothetical. As far as I know this has not happened yet.

The Supreme Court in Hobby Lobby said that employers can avoid statutory obligations (e.g. paying for health insurance which covers contraceptives that destroy fertilized eggs, otherwise termed "abortifacient" contraceptives) if following the law would substantially burden the exercise of their religion. In the Hobby Lobby case, the employers won and now will not have to fund insurance for abortifacients.

What about other laws, and other employers? Mennonites, for example, are conscientious objectors, and owners of large businesses. Should they be allowed to deny a Reservist's right to get his or her job back after a deployment because supporting war violates their religious principles? The law that requires this is called USERRA, you can read about it here: http://www.dol.gov/vets/programs/userra/.

There are other examples: some believe God commanded the races to remain separate (i.e. KKK); some religions do not permit vaccinations or surgery; some do not permit unwed couples to live together.