"Judge not" in Matthew 7:1 isn't about keeping your religion private or about keeping silent on public immorality. It's about cutting people some slack and not being a hypocrite. We are commanded to discern between right and wrong, clean and unclean, to proclaim these truths publicly, and to warn our neighbors when they are straying. We are also commanded to love one another. It's important to strike an appropriate balance.
Gray areas are ubiquitous in Torah. It's possible to stand for what's right and still allow others room to disagree on matters of theology. It's a matter of humility. It takes humility to acknowledge one's own flaws and to make allowances for the flaws of others.