Not a constitutional lawyer, or a 2L, so take this comment for what it is worth. Under ACA, a company has to either cover its employees or pay a fine. The SCOTUS has determined that the fine is a tax. If the employer has religious objections (or any other kind of objections) to buying the insurance, the employer can pay the fine. Thus the law and the penalty is religion-neutral - it doesn't target religious scruples, or business scruples, or I-just-think-insurance-is-a-scam scruples, it presents a binary option and doesn't inquire as to why you make the decision to pay the fine.
Every year in this country we all pay taxes and those taxes go to buy things that many of us may be religiously opposed to - contraception for government workers through their health plans, bombs to kill Pakistani children. We don't get to carve out religious exceptions for that.
Leaving aside legality for a minute, the arguments made by Hobby Lobby seem to totally ignore the agency of the employee. The employee is making the decision to use birth control. How there is a principled distinction between paying an employee a salary which she uses to buy birth control, vs. channeling that money into an insurance policy that indirectly pays for the birth control? I am giving the employee a package of income and benefits to induce her to work for me. Same money either way, the choice is up to the employee, not the employer. What she does with that package of benefits is between her and God, not between me and God.
Put another way, I cannot understand how the owners of Hobby Lobby think they're going to come up to the Pearly Gates and St. Peter will say "sorry, some of your employees used their insurance to buy birth control, say hi to Lucifer for me". That kind of religious thinking makes no sense to me as a Christian.
ETA: some religions don't believe in things like blood transfusions and some pastors have been known to preach against vaccines. Are we going to allow companies (or individuals) to opt out of Obamacare for these kinds of religious scruples that most people acknowledge are off-the-reservation crazy? Because if you allow an exception for contraception, I don't see how you can deny an exception for the anti-blood transfusion people. Maybe there's some kind of principled distinction there that I am missing, but if the point is to allow for freedom of religion how can the government pick and choose between sincerely held religious beliefs? Answer: it can't.