Some people challenge liberty of conscience on grounds that some claims of conscience are faulty. But shouldn’t the state bear the burden of proof if it seeks to interfere?
It would be difficult to defend the absolute claim that the state may never, under any circumstances, compel a person to do what he considers wrong. Some nut may say he considers it wrong to stop at red lights. But I think you are exactly right to emphasize that if the state does seek to compel a person to do something he considers wrong, the burden of the argument should lie on the state. The presumption should lie strongly with the individual.
This forces the state to make a moral argument in terms of precepts that are right and true for everyone and accessible to reason, something the state is loath to do because it pretends not to have a moral position. Its pretense is aided by the way the term “autonomy” is now used. Though the term has no single, precise meaning, it functions in two chief ways.
First, it functions to obscure the distinctions among a variety of radically different moral ideas, some of them defensible, some of them not. For example, sometimes the term “autonomy” is used for the idea that people should have the broadest possible liberty to do what is good and right -- a liberty which Sean Murphy of the Protection of Conscience Project more adequately and accurately calls “perfective” liberty of conscience. But others use the term "autonomy" for the idea that individual behavior should be exempt from judgments of good and evil. Obviously these ideas are antithetical.
The solution here is to disentangle the ideas. In each case of entanglement, instead of speaking vaguely of autonomy, we should identify the specific moral idea that the term “autonomy” is being used to promote.
Second, the term functions to conceal the moral grounds on which the state seeks to coerce someone to do something. In such cases the term is used as a synonym for moral neutrality, which of course does not exist. For example: The state guarantees the freedom to have an abortion, but denies the freedom to refuse to participate in an abortion. In defense of the first action, the state says of itself that it is not making a moral judgment, but merely protecting autonomy. In defense of the second action, the state says of those who refuse to participate that they are enforcing their personal moral judgments, and denying the autonomy of others. Nonsense. The state’s actual moral judgment – unargued, because the state pretends that it isn’t a moral judgment -- is that it is morally permissible for private individuals to employ lethal violence against a certain category of unprotected persons, and that it is morally impermissible for other private individuals to refuse to help them do it.
The solution to this problem is similar to the solution of the other one. In each case of mendacity, instead of letting the state get away with pretending to have no moral stance, we should translate the obfuscatory language that it uses into clear language that says what it means.