Preliminary Note:
It should be noted of course that conscience involves what one must do or must not do, not what one might want to do. Freedom is the ability to do as I ought, not to do whatever I feel like doing. It involves duty, not self-gratification. Because of this, it would be wrong to interpret the freedom of conscience as the justification to do whatever I want to do. Conscience tells us "I must do [X] because it is good, I must not do [Y] because it is evil." It doesn't tell us, "I don't feel bad about getting an abortion, so I'm just following my conscience." It is unfortunate that America confuses conscience with self-indulgence.
The Threat
The thing that concerns me most about the Obama regime and the attempts to impose their will on people who feel conscience bound to refuse to obey is not the threat to the Church. We may end up small, poor and persecuted, but we will survive whether Obama is reelected or not. No, what worries me is the extreme recklessness of the supporters of the HHS mandate who seem to be so short sighted as to be unaware of what the significance of this attack is.
The fact that the government thinks it can impose its views on people who are morally bound to disobey under the claim that there is more benefit than harm done shows a very dangerous fact:
If the US government believes it can set aside the conscience of an unpopular group for the benefit of "the people," then there is no limits to what it can set aside in the name of "the good of the people." That includes the Constitution itself.
After they come for us, they will eventually come for you
Even if the reader should reject the Catholic position on the HHS mandate, they should recognize that if the attack on conscience is allowed to stand, then there is nothing to stop a future government from invoking "the good of the people" in demanding compliance with the law they see fit.
That's right. Both political parties can make use of such a precedent to justify what they want. Today's liberals who cheer the HHS mandate may be shocked when the wheel eventually turns and conservatives get control of the government and start using this tool to start attacking what they dislike.
This isn't speculation. History tells us of governments which rejected conscience in the name of "the good of the people." We used to recognize these governments as Fascist or Communist. We used to know that these governments would steamroller the conscientious objectors, labeling them as enemies of the state for "imposing" their "bourgeois," "reactionary" attitudes on "the people."
The Fascist and Marxist governments believed the rights came from the state and the state could take away those rights. In contrast, Americans believed that human rights were inalienable. They couldn't be taken away by the State, because they came from a source higher than the state. A government which tried to take away such rights was recognized as unjust and had to be opposed.
Partisanship blinds us to this danger
Unfortunately, partisanship has reached the point that the prevailing mentality seems to be, "Whatever I do to harm my enemy is acceptable. Nothing he does to harm me is acceptable." You can't build a just society on such a partisan mentality. You can't build a free society on such a mentality. Such a society must eventually become corrupted, where one faction is perceived as evil solely because it isn't a faction a person disagrees with. Conscience is replaced by self indulgence.
It is also a danger because those people who do truly follow what is right are confused for partisans. "You oppose abortion, Republicans oppose abortion, therefore you are a right wing Republican!" It is also a menace for those practicing the faith. The Church position on contraception and abortion is seen as "right wing" and the Church is denounced by the political "Left." On the other hand, the Church position on immigration is condemned as "left wing" and the Church is denounced by the political "Right."
When a whole nation makes use of these hostile labels to attack what they dislike, we have lost the ability to look for truth. We become blind to the fact that the Church can be motivated by what is necessary for salvation and not "increasing the Sunday collections" or "wanting to suppress women." When we look at the world through a partisan lens, we have an obscured view.
Objective Truth Exists
However, things that are true can be known, and it is also true that moral things can be known. Things that are true by their nature are always true regardless of time or place. So if the concept, "slavery is wrong" is objectively true, that means it was wrong regardless of whoever practiced it in the past, and it would be objectively wrong to practice it in the future.
However, if the statement, "slavery is wrong" is not objectively true then it means that it was right in at least some circumstances in the past and might be right in some circumstances in the future.
Likewise, the principle of "We must always follow our conscience." If this is not objectively true in all times and places, then it means there can be a time or a place where it is acceptable where one can deliberately do evil or refuse to good for a higher cause. We've had nations which operated under such principles – nations where I would not care to live.
QED
This brings us back to the original point, from a different angle. Without the concept of objective right and wrong, a government can invoke anything they choose under the justification of the greater good, and can force a person to comply. Who defines the greater good? The government which is forcing people to disobey their conscience or suffer repercussions.
Thus every person should see the danger of tolerating a government which places itself above the freedom to do what is right.
Quis custodiet ipsos custodes?