I'm posting an answer I gave to a correspondent, on the religious liberty issue:
i) I don't think it's necessary to cast the issue in double effect terms. Although that's a useful principle, it can become unnecessarily complicated.
I think a simpler argument would involve conflicting duties. Take prior obligations, like dependents. You have a duty to protect and provide for your dependents. That may come into conflict with a prima facie or ceteris paribus obligation to avoid complicity in evil.
In cases like that, a higher obligation overrides a lower obligation.
ii) Complicity in evil is tricky since, in a fallen world, complicity in evil is unavoidable. It's a matter of degree:
9 I wrote to you in my letter not to associate with sexually immoral people— 10 not at all meaning the sexually immoral of this world, or the greedy and swindlers, or idolaters, since then you would need to go out of the world. 11 But now I am writing to you not to associate with anyone who bears the name of brother if he is guilty of sexual immorality or greed, or is an idolater, reviler, drunkard, or swindler—not even to eat with such a one (1 Cor 5:9-11).
We have to pick our battles:
Of course, there are complications here, as well. For example, we can distinguish between permissible involvement in someone else's transgression and impermissible involvement in someone else's transgression, and we can ask whether both or only one of these ways of being involved undermines one's standing to blame. Patrick Todd (2012) argues that only impermissible involvement undermines one's standing to blame, and to illustrate his point he imagines two Nazi commanders, one of whom is committed to the Nazi cause and the other of whom is using his position of power as an attempt to undermine the regime. If, in order to keep up appearances, the latter commander issues an order for a subordinate to perform an action that is morally impermissible, does he lose his standing to blame the subordinate? Todd claims that he doesn't, and thus that there is an important distinction between complicity that undermines standing and complicity that doesn't.
Gregory Mellema (2006) provides a very useful way of assessing different levels of individual contribution by distinguishing between six different ways in which individuals can be complicit in wrong-doing. According to Mellema, individuals can induce or command others to produce harm. They can counsel others to produce harm. They can give consent to the production of harm by others. They can praise these others when they produce the harm. They can fail to stop them from producing it.
A second way of tackling the distribution question in this context that does not seem to violate the principle of individual freedom is to look, not just at the particular role that individuals played in their community's production of harm, but at how much freedom the individuals had to distance themselves from the community that has done wrong. Here we might want to use voluntariness of membership as a criterion of responsibility. Jan Narveson (2002) does so himself in his generally skeptical work on collective responsibility. Narveson argues that in thinking about the responsibility of individuals for group harms we need to be careful to distinguish between four different kinds of groups, namely: those that are fully voluntary; those that are involuntary in entrance but voluntary in exit; those that are voluntary in entrance but involuntary in exit; and those that are voluntary in neither respect. As Narveson makes clear, responsibility is diminished, if not eradicated, as we go down this list.
iii) As I've indicated elsewhere, I think it's permissible for a Christian small businessman to lie in situations like this. I think that's a morally permissible form of civil resistance to unjust or immoral demands. That doesn't necessarily mean it's obligatory in those situations.
iv) I think some Christians or organizations have a greater responsibility to resist tyranny than others. Some people have less to lose than others. To take an extreme example, a Christian with terminal cancer. Not much the gov't can do to him.
Some people have fewer prior obligations or social responsibilities (e.g. dependents) than others. They can assume a greater personal risk without harming others in the process.
Some individuals or institutions have the wealth, popularity, and or legal authority to put up a more effective resistance than the easy marks that gay/trans lobby picks on, viz. Alabama Supreme Court, Duck Dynasty, Chick-fil-A.