When I read news articles like this one:
Judge rejects Mennonite firm's healthcare law challenge
It makes me wonder why people often claim a for profit company cannot have religious views. There is plenty of precedent for businesses have other personal attributes and constitutional protections.
My Business, Myself: Piercing the Corporate Veil | Culture | Religion Dispatches
Citizens United v. Federal Election Commission - Wikipedia, the free encyclopedia
Corporate personhood - Wikipedia, the free encyclopedia
The above articles show that businesses sometimes get personal rights and sometimes they do not. Obviously, from a legal perspective, this is still a gray area that will change as the future progresses. In my opinion religious liberty is worthy of being protected even when attributed to a business.
However, I do see a slippery slope of non-religious businesses taking advantage of religious exemptions or protections. Therefore, I think a reasonable compromise would be that exempt businesses: must sign an affidavit, display a mission statement with clear religious goals (on their website and place of business), post a sign stating, "this is a religious organization.", and lose their exemption if fraud/dishonesty of their mission statement/affidavit is detected. This would make abuse a lot less likely. Potential abusers of exemptions would have to be willing to publicize their choice to their patrons and possibly deal with negative public reactions.
Obviously, my proposal with have weaknesses of its own, but I think there is a way to reasonably accommodate religious liberty for a business. If you disagree, just take your money to the non-religious businesses. We still have the right (at least for now) to choose what businesses we shop at.