Interesting point. What you are essentially saying is that because a claim of religious conscience impacts the eternal life, it automatically gains more power in the present then a claim of non-religious conscience. This while both claims have the same moral/ethical standing, so should impact the eternal life in the same way. By the way, not all non-religious claims of conscience are made from the conviction that one needs to behave ethically to be feel right in your own skin. One can also be convinced that one needs to behave ethically at all costs, because it is for the greater good.
Further into the interview the author gives 3 distinguishing qualifiers that determine what religion is as opposed to anything else. They are
1. Categorical demands on adherents which are both absolute and non-negotiable
2. Some beliefs that are isolated against ordinary standards of reason and evidence (such as transubstantiation)
3. All religions are discharged by forms of existential consolation. They teach us how to deal with death, loss, pain and suffering. So, in the example he uses, the Sikh boy vs. the Farmer's son, the Sikh boy's claim to be able to carry a Kirpan is not just a demand made by his religion which rules his eternal life, it is also a cultural demand that proves his manhood. For the farmer's son, it is simply a family tradition. There is more weight on the side of the religion, thus more pressure on the individual to conform and more stress and harm caused by disallowing the knife.
No! Fish, in the article I've linked elsewhere in the discussion does a much better job than I could in defeating these pro-religion exemption arguments: The familiar proverb that captures this requirement is, “Ours is a government of laws and not of men.” The liberal project is threatened whenever that formula is reversed, whenever the state’s generality is at risk of being eroded by the particular beliefs of men. Substance, then, is the chief danger to the liberal state, and the chief form of that danger is religion, both because of the categorical demands it places on its adherents and because it refuses the formal constraints that keep substance cabined in the sphere of the private. So that while the liberal state is pledged to refrain from burdening the claims of conscience, were it to surrender itself to them, it would, says Leiter, “cease being a state.” Just such a surrender would be involved in the “carving out of special protections” whenever someone wholly in the grasp of conviction — religious or any other — demanded them. So in short, whenever we offer a conscious exemption to established law based solely on religious or cultural tradition, liberalism itself is the big loser.Liberalism begins by dislodging the authority that in other political systems provides stability and meaning — a God or a theology or a monarch or a dictator. Liberalism replaces those rejected authorities with the idea of individual rights and it becomes the liberal project to build a political system and a system of value on that foundation. Somewhat paradoxically, the privileging of individual rights means that the substantive commitments of no individual can be allowed to inform the body of law, which must be generally applicable; applicable, that is, to every citizen no matter what his or her beliefs and biases may happen to be.