This line is uttered by Deputy Governor Danforth in Act Three. In my edition, the Penguin, it is on page 94, just after Francis Nurse has submitted a testament signed by dozens of people that attest to his wife's and Martha Corey's good reputations as Christians. Danforth has ordered that all signers be arrested and brought in for questioning, and Nurse fears that he has brought trouble to their doors in asking them for help. Danforth says,
No, old man, you have not hurt these people if they are of good conscience. But you must understand, sir, that a person is either with this court or he must be counted against it, there be no road between. This is a sharp time, now, a precise time -- we live no longer in the dusky afternoon when evil mixed itself with good and befuddled the world. Now, by God's grace, the shining sun is up, and them that fear not light will surely praise it.
In his Puritanical logic, he assumes that anyone who is innocent has nothing to fear from the court: if an individual is guilty of nothing, then the court will not, cannot, harm them. Danforth believes that he and the court are doing God's work, as it is "the entire contention of the state [...] that the voice of Heaven is speaking through the children." Therefore, if you are against the court, then you must be guilty because the court is good. If you are guilty, then you are bad and not on the side of God, and it is the court's moral duty to find you out and punish you. It is a very black and white perspective, not allowing for corruption among the magistrates or ulterior motives on the part of the accusing girls or their families.