The current protections for religious entities in the health care law are so limited, they provide inadequate protection for the freedom of religion for proprietors of said religious entities.
The HHS mandate would require faith-based institutions to provide contraception against the teachings of their faith. It's different from a health care treatment as many institutions have well delineated exceptions: i.e. Georgetown provides birth control to women who require it for health reasons but not for contraception.
Employees are free to seek work elsewhere due to their beliefs but under the HHS mandate, employers are not entitled to the same freedom.
This is a clear violations of the protections afforded to the citizenry by way of the First Amendment.