While I understand what you're getting at Mleake. In the case of Thoreau, I think most would point out he did accept and understand the consequences of his decision to not pay taxes(going to jail). Also that his situation was not remedied by his objections being recognized as just, but by someone paying his taxes for him.
I'm not so sure that many of those who might object to universal background checks would be quite as willing to accept the consequences of their actions and be preferential that no remedy be rendered until their actions were determined just. Coincidentally, I also don't think they'd have volumes of well written prose describing their personal philosophies and reasoning for their conscientious objection.