First of all, the logic under which the law extended those rights to corporations contains a fundamental error: namely that a corporation is not able to exercise certain rights in any meaningful sense.
Consider the following: A corporation is a legal construct. It is not a person, and it cannot exercise autonomy from the persons who operate it.
When was the last time you saw a corporation walking down the street, or having a coffee with a friend in a café? The fact is you haven't seen it - ever. It doesn't happen. Yes, a corporation exists, and has a certain reality associated with it. However, we should never make the mistake of assuming that it is anything other than a legal fiction.
The error was made ages ago when the US passed a piece of legislation which effectively defined a corporation as equivalent to a person for all intents and purposes, a definition which was referenced explicitly in the RFRA act that seems so central to the Hobby Lobby decision. Since then we have seen a series of cases where corporations have asserted that they must have access to human and civil rights under the law.
Hobby Lobby is just another incremental expansion of those rights, and it is perhaps the most concerning yet. Few would disagree that there is a reasonable right for a corporation to have access to free speech, or fair trials under the law. This decision now extends to the corporation the adoption and exercise of rights related to religious freedom.
Consider for a moment the grand irony of such a proposition. In what universe can we imagine a legal fiction being able to adopt or practice any particular human faith? You will never see that corporation sitting in a church, or otherwise engaging in worship. The very idea that a corporation can be said to be "religious" in any way is ludicrous.
Granting a corporation the right to exercise the "proxy right" to reflect the religious beliefs of its ownership is also problematic. First, the understanding of religious beliefs is highly variable. Second, the expression of those beliefs is highly individual. Third, the concept of a "religious belief" has no objective and reasonable test that can be used to establish its validity. A religious belief is whatever the person who claims it says it is.
While we might commonly think of these rights in the context of a Judeo-Christian understanding of what a "religious belief" is, one has only to look at the breadth and depth of human spiritual/religious thought over the centuries and millennia to realize that there are many "beliefs" which could be asserted that are arguably repugnant.
As has been demonstrated time and again by the decisions of corporate management and boards, at their most fundamental, corporations are inherently sociopathic. They exist to make their owners money first and foremost. That means we get decisions such as those we see where health insurance providers do everything in their power to deny treatment; or decisions like those around the Ford Pinto's fuel filler get made.
These are not the decisions of individuals. They are the collective decisions of committees of people - people who are at the end of the day held accountable to the financial performance of the corporation. For the management of any corporation to sit there and pontificate about how this or that practice is "immoral" and insist that the corporation must reflect those "moral" beliefs, when ultimately no corporation exists for any purpose other than making its owners money.
It is my opinion that while there are legitimate rights for corporate entities, those rights must be described separately and apart from the individual rights held by citizens. Further, those rights must be held as subservient to the individual rights of a country's citizens.
The Hobby Lobby decision allows a corporation's asserted rights to supersede those of the citizens who work for the corporation. This is an error not of the application of law, but of the creation of law itself. It is unfortunate that the SCotUS did not acknowledge this in its decision or on its blog.