I think that it is simply an example of how a complex law like Obamacare, due to lack of diligence in crafting it, ends up endangering both freedom of speech and freedom of religion in one fell swoop.
It could set a dangerous precedent in allowing govt to make a law that interferes with freedom of religion. Not to mention compounding the threat by disallowing someone to speak out against the law's unconstitutionality.
If Obama gives an exemption, that doesn't change the law's unconstitutionality. I think the law has to be made consitutionally correct. For example, suppose a small business run by an RC owner did not wish to offer abortion as part of health care insurance, would they also be exempt from the law? What happens to them if each has to pursue an individual exemption?