That is why it was a CATCH-22 situation Obama/Sebelius/Reid/Pelosi did this intentionally so that EWTN, Wheaton College, Little Sisters of the Poor, etc, can say they don't want to provide coverage, but their insurance company will regardless of whether the employer opts out or not.
LifeSiteNews.com had an article about this on EWTN:
Judge rules against EWTN in HHS mandate case
This was on June 19, 2014 before the Hobby Lobby Ruling.
The Judge, from the article states:
"EWTN doesn't have to comply with the mandate. All it has to do is sign a form certifying its opposition to the use of contraceptives and then deliver that form to its third-party administrator," she continued.
Further down in the article [Reporter Ben Johnson writes]:
The Obama administration's health care “accommodation” requires employers to certify their religious objections, but their insurance company must then offer female employees birth control pills for “free.” Critics say the move is nothing more than an accounting gimmick, but Judge Granade found the distinction compelling.
The article states that contraceptives that cause abortions must be offered...
So Obamacare, as originally legislated, must provide abortion-causing-pills...
What Alito said is that they do not have to sign a form. They simply say we’re not providing this coverage, and it’s over for them.
That is a distinction that makes a difference. It is saying, “No” and having it mean no.