Two different consciences

While I was reading On the Duty of Civil Disobedience, I noticed that Thoreau had stated that "Must the citizen ever for a moment, or in the least degree, resign his conscience to the legislator?" (Thoreau 1017).  The basic message of this rhetorical question is that when a citizen thinks the government is committing amoral actions, then that citizen should be able to follow his or her conscience to be able to resist the government.  Thoreau even elaborates on this message throughout the rest of his essay.  He mentions of how he strongly disapproves of the Mexican-American War and slavery, yet both of them had strong support from many Americans during his lifetime.  He is basically following his own conscience not only by expressing his disapproval of the Mexican-American War, but by "[paying] no poll tax for six years" (Thoreau 1025).  However, there are some flaws when Thoreau's concept of "right and wrong" is applied to certain situations, especially the 2016 election (Thoreau 1017).

Speaking of flaws, I do not mean that Thoreau's concept of "conscience" is flawed, I mean that there is some complexities when his ideals are applied to the 2016 election.  Most of the Democrats, for example, passionately support Hillary Clinton.  They support her because she advocates LGBT rights, gun control, and even abortion.  They support her because her policies would likely change the country for the better.  They are following their conscience as they support her.  On the other hand, many of Trump's supporters are actively against LGBT rights, abortion, etc.  That's because many of them are Christian fundamentalists.  They believe that if they support Trump, they would "make America great again" and correctly follow the ideals in the Bible.  They are actually following their own "conscience".  Many liberals (such as me) would denounce the Trump supporters' "conscience" as bigotry (and vice versa).  So when the debates happen between Trump and Clinton, they sort of represent the Democrats' "conscience" clashing with that of the Republicans.  They represent two different mindsets willing to fight each other for almost eternity.  But if Trump gets elected as president, does that mean the liberals should follow their "conscience" by refusing to pay their own taxes just as Thoreau did?  Or if Clinton gets elected, should the conservatives use their own method of civil disobedience?

Note: Please do not get the impression that I am a Trump supporter, I actually dislike Trump very much.