The problem is when does conscience alleviate any requirement for you to obey the law?
One of the problems is in the word "conscience" since that presumes some moral standard, and Marotta's sentence doesn't give us a context regarding the moral standard or the life situtaion.
We start from the premise that there are some moral values that are objective, absolute and universal. And as Objectivists, we hold life, a flourishing life, life as is appropriate to a human, as our standard of value.
That is important, because when we arrange these primary values into a hierachical scheme, we will put life-in-a-lawful-society somewhere in the list. It will be a value that is less than life itself, therefore if the government were trying to kill us, for some reason, then we would not accede to the very law that was trying to end us. It is about a rational ordering of values for life here on earth (and not in a lifeboat). We arrange values in a hierarchy for that purpose. And when we find a conflict, we look for errors in logic, errors in the understanding of the value, or we see that to remain true to value A would violate value B and the hierarchy tells which way to go.
And it gets a bit more complicated because our acts have consequences. The reason I don't drive faster than I normally do isn't because I have a sense of duty to obey the speed law and am being spoken to by my conscience. It is because I don't want to pay a speeding ticket. I may or may not recognize some moral right of the government to set a limit on a given street that they manage. However they manage it with involuntarily collected taxes - which is not very moral of them. And the specific speed limit might seems too low to be reasonable and respectful of my time.
But there are two strong moral values that will prompt me to either not speed, or to accept a ticket gracefully if that is the case:
1.) Respect for the concept of rule of law - I don't not value an environment where whim and initiated force are the rule,
2.) It is NOT in my self-interest to complicate my life with a legal battle to fight a speeding ticket.
The people at Hobby Lobby are clearly very religious and very opposed to funding birth control. They have a moral hierarchy of values where obedience to those moral values comes higher than the complications and costs of fighting the law. But they did fight it in the courts. They didn't go anarchist or rebel.
Do you have a moral right to evade taxes? Your moral duty is to your self-interest. So, if evasion of taxes gets you put in prison, then you didn't serve your self-interest very well. If your income tax were less than 1% of your income, then fighting it on principle might be in the service of moral political principles, but is it in your self-interest at that point in time? If the tax is 95% percent it is a different story. It stays an immoral tax, just more so, but now, the fight for the moral political principle may well coincide with your self-interest. It can be immoral of a government to prohibit a certain action, yet moral for a person to not throw himself in front of the juggernaut in an attempt to stop it (I believe that was Rand's description).
Remember Vietnam - It was a moral war in the sense that it was fighting against a communist aggressor nation, but it wasn't in the national interests of the United States. Even if the war was moral it wasn't moral to draft young men to fight it. Someone could be moral and acting in their self-interest when they joined to fight, or if they protested the draft and fled to Canada - it would depend upon how they had arranged their hierarchy of values and they stayed focused on their self-interest.
If you can be exempt from taxes on the basis of conscientious objection, then, as the Supreme Court ruled in Reynolds, even human sacrifice would be allowed. And in that court opinion, it was also asserted that law officers can stop a widow from immolating herself on her husband's funeral pyre. The libertarian claim that you have an absolute right to commit suicide is fallacious.
The supreme court should be weighing the intent of the founders as represented in the text of the constitution. They should be deciding if the first amendment speaking to religious freedom exends to ignoring other laws. Are the other laws constitutional? You say that a person does not have an absolute right to commit suicide. Assuming that the person is an adult (has their full set of rights), and is rational, then to say they cannot commit suicide is to say that they do not own their body or their life and that the government is the owner (or God, or society, or the nation). That would be the opinion of progressives, fascists, the religious right, but not Objectivists.
The government has a compelling duty to protect those who cannot protect themselves. Children and the aged are easy examples. Anyone who exhibits irrational behavior can be (and should be) prevented from harming themselves.
Objectivists think in terms of individual rights. Children and people who are mentally/physically unable to exercise choice are not seen as agents able to act to protect their own rights. We have in our law, a recognition of this where we establish custodial care. Parents (or guardians) are the custodian of a child's rights. Government only steps in when a child's rights are being violated and then, a special case is made where the parent or the guardian is the violater. We do something similar for the aged who cannot care for themselves. In a hospital there is a chain of custodial duty that evolves out of familial relations, spousal relations, doctor-patient relationship, etc. When a person is in a medical setting, and in a coma or otherwise unable to exercise choice, there is a means of determining the legal custodian of that person's rights. There is NO compelling duty that magically arises in some altruistic context. No. Instead we create a set of laws that protect individual rights. That is where these laws come from. Just as civil courts provides a mechanism to right wrongs without recourse to the use of violence. Why do this? Because without it, individual rights would be at risk.
Just laws arise out of individual rights. Protection of individual rights is the purpose for creation of laws. Altruism has held sway for many years and in doing so obscures the fact that it is not the reason for providing protection.