Weird! I was just writing about freedom of conscience in relation to the abortion issue when I decided to take a break and check my email and Fluther.
Freedom of conscience is the freedom to decide for oneself what the good and the right are. It seems Martin Luther did not believe that he was free in this regard; he claimed that he had no choice but to to believe what he believed. It’s interesting that the rise of capitalism coincided with attempts to redefine freedom (in theology by Luther and Calvin, in philosophy by empiricist philosophers such as David Hume).
The hard part is figuring out what freedom of conscience means politically/legally/constitutionally. Forcing citizens to belong to a state religion is obviously a violation of freedom of conscience. What about taxing people to fund policies that they oppose on moral grounds, or requiring medical professionals to perform procedures that they object to, or teachers to teach content that they disagree with? And so on. We want to let people follow their own lights, but the state cannot be neutral on certain issues, and therefore it will favor certain conceptions of morality over others.