As others have pointed out..
The rider merely clarifies that they are NOT creating a blanket rule because different religions have different views. So it's really the exact opposite of what you are saying. Instead of imposing one religious view on everyone, they exempted other religions from the ruling while opening the door for those religions to litigate should they feel it necessary.
Again...they ruled on the case in front of them.
Honestly...there is a fix. Just have the Feds, via Obamacare, PAY for contraception. It (Obamacare) was passed half-arse, written half-arse, and the website wasn't even done that well. They haven't been varifying citizenship or income until now. So how hard could it be to do a half-arse job of covering contraception?