First Amendment rights are limited when there is a direct adverse effect on other people - like shouting "Fire" in a crowded theater when there is no fire. The choice of a business owner to offer or not offer specific employment benefits should not even require First Amendment protection. Note that there is no discrimination in the particular example of whether or not a health insurance plan covers abortion related medications. If anything, the plan discriminates against men since they don't get the same benefit.
Private health insurance plans have a variety of limitations and covered and non-covered items. Why is the government involved in this at all? There is no harm to the employee from not getting many particular benefits, since they may never even use it, and in this particular example the cost of the medicine in question is minimal, and the "benefit" not being offered to the employees is, taken over the whole of the employees, negligible. Nobody that is employed needs insurance to protect themselves from a $50.00 risk.
Put another way, the government is proposing millions of dollars of fines because the employer won't agree to pay for a $50.00 pill that some small percentage of its 13,000 employees may rarely buy. Assuming half of its employees are men, 6,500 employees could potentially use a morning after pill. But of the women, no doubt some are too old to need such a thing, and many are married and also not as likely to be interested in a morning after pill. Some women of course are already using birth control. So for the men, the benefit being "denied" is of no personal value. For the women, it is the probability that they need or want the morning after pill times its cost. Overall I doubt you can show any harm to any employee from the lack of the benefit, and hence logically there is no reason to compel insurance for it.
But that's not the logic behind the law. The goal of the law is to force acceptance of a particular political viewpoint advocated by liberal Democrats, using huge fines as the hammer to force people to give up their values and viewpoint.
Do you even know where that "example" came from? It came from Schenck v. United States, 249 U.S. 47 (1919); this case was about upholding sedition laws for WWI which restricted political speech -- exactly the sort of speech the 1St Amendment was meant to protect -- protesting the war. (The case was wrongly decided, basically saying: the congress can do in war what it cannot do in peace.)
The whole "fire in a crowded theater"-argument is one that justifies that which is not justifiable: it is the expansion of "legal reading" of the Constitution to mean that which is not said. -- For you to use it only perpetuates the evil.