Regular readers of this site won't be surprised to learn where I stand on this issue. Public officials have a duty to abide by the laws of the land. My tax dollars as a gay man go to finance their salaries and therefore marriage commissioners must be willing to abide by our country's equal marriage laws.
I do think, where possible, such commissioners with strong religious beliefs should be able to pass along duties re: same-sex nuptials to other commissioners who don't share their feelings. Such a compromise wouldn't even need to be declared as long as the same-sex couple receives the public service they are seeking. But in remote areas where marriage commissioners are hard to come by and no alternatives are available, it's clear that those employed by the government to carry out these duties must live within the law. If they are unwilling, they should resign their posts. Period.
Orville Nichols's lawsuit will form an interesting test case on this issue. If previous rulings on the issue are any indication, he doesn't have much hope of succeeding.