I think Hobby Lobby should-- and I cautiously predict, will--win this case, but the "200 years of precedent" the author talks about is far more mixed than the article lets on. Corporations have always been understood to have certain constitutional rights, chiefly those relating to protections of property rights. There are also certain constitutional rights that corporations clearly do not have, such as the privilege against self-incrimination. There are certainly gray areas in this field of law.
For example, individuals who operate a corporation retain attorney/client privilege while the attorney/client relationship between the corporate entity and an attorney has no where near the same degree of protection.
The few gray areas that exist are very small and in fact most have equivalents in law as it relates to individuals in some circumstances.