Moreover, since health insurance is part of the employee compensation package, it isn't the employer paying for it anyway.
You don't understand. See, if the employer pays a sum of money to a third party insurance company and that insurance company uses some small fraction of that money to pay for certain methods of birth control as part of a larger employee compensation package, it is a much more direct method of paying for these contraceptives than if the employee just cashed their check at the bank inside their local Kroger and then took the money to the pharmacy counter to buy some Plan B pills.
This is about accountability to God, after all. If you're the Hobby Lobby folks and you wind up at the pearly gates one day, no doubt St. Peter is going to ask if you paid for any sort of maybe abortion providing medicines with the money you made selling cheap Chinese trinkets.
As such, it is very, very important to be able to say "no, we didn't pay any intermediaries any money which people could choose freely to spend in part on nasty abortion stuff...we paid those people directly."
Perhaps a minor distinction to some, but we're talking about souls here.