I used an absurd example to show that your interpretation of the decision ("People can now freely exempt themselves from laws they deem violate their religious convictions. Solid case.") was absurd.
It isn't. You can call it absurd all you want to, but having a general sense of how the law actually works, I can tell you for a fact that this ruling will impact federal law regarding discrimination against homosexuals. Trust me, I know.
The law specifically impacted will be this one:
42 U.S.C. 2000a
(a)
Equal access
All persons shall be entitled to the full and equal enjoyment of the goods, services, facilities, privileges, advantages, and accommodations of any place of public accommodation, as defined in this section, without discrimination or segregation on the ground of race, color, religion, or national origin.
It can be gleaned here that people can and will file for an exemption based on this law, because such compliance would violate their religious beliefs, they will cite the Burwell v Hobby Lobby case as precedent.