Am I missing something…?
Calling them “benefits” does not exclude them from packages of “compensation” for work – earnings.
If the owners of a business have “sincerely held” religious beliefs that are in opposition to the basis upon which a law rests (access, affordability, preventative care), or some effect of that law, then they should tithe the “cost” from their “profits”, not from the payment they have contracted with employees to provide (within the purview of civil law).
I think that the whole notion of "not entirely for profit" is the real issue here (because the "burden" is borne by workers as much as employers in the SCOTUS decision). A "religious employer" is a strange notion, but too obvious a blunder, I suspect.