If you've actually read the opinion, nothing is being forced upon the employees as they still get their emergency contraceptive and IUD coverage, just via the same mechanism that Obama already set up to handle non-profit corporations with religious concerns that those particular methods might actually be abortive in their manner of action. (Indeed, Hobby Lobby wasn't seeking exemption from covering all forms of contraception as some religious groups were, but four specific ones over which the question of how they work is disputed. AFAIK, the family that owns Hobby Lobby has no problems with contraceptive methods that prevent ovulation.)
And then on Thursday, SCOTUS granted Wheaton College an injunction to allow it to not comply with the process you outline above.
True, but it doesn't change the fact that their employees still get the contraceptive coverage.