Despite the freedom of conscience and homage, individuals are still obliged by the social compact to observe what Locke calls "duties they owe one another," or as Virginia's Declaration of Rights puts it:
"That religion, or the duty which we owe to our Creator, and the manner of discharging it, can be directed only by reason and conviction, not by force or violence; and therefore all men are equally entitled to the free exercise of religion, according to the dictates of conscience; and that it is the mutual duty of all to practice Christian forbearance, love, and charity towards each other."
Totally, Locke lived by two Great Commandments, Love God with All the Strength of Your Being, and Love Your Neighbor, Your Brother and Sister as Your Self. He also Established Non-Violent Civil Disobedience, accepting the Consequence, as a Tool of Protest against Injustice, where All Else Fails.
The Point that gets missed, here is more brought out in "The Emperor Has No Clothes". When you squash the Individual to bend to the will of Society beyond Reason, to the point that they prefer to to deny what they witness, for the sake of acceptance, you have committed a crime against the forces that govern creation. Part of the reason we are here is improve ourselves through cause and effect, through learning and knowledge. Another reason we are here is to Witness, and tell the honest truth about what we witness, from our own individual perspective, which we each possess separately. To mess with that for the sake of conformity, expediency, or anything else is a disservice to the individual and the group both, whether we see it or not. The Freedom to Speak the Truth. Unalienable Right. Our Obligation to Our Creator, takes Precedent over Everything Else. As a Christian or Jew, the First Two of the 10 Commandment's are Crystal Clear. When one needs to deny their faith or deny the truth as they witness it, or deny their Conscience to belong, it is not worth belonging.