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How should we handle atheists who attack the church?

Woe to them! They have taken the way of Cain; they have rushed for profit into Balaam’s error; they have been destroyed in Korah’s rebellion.  Jude 11
            People who attack the faith have been around for a long time.  Jude, the second to the last book of the Bible, refers all the way back to the first five books of the Bible to give examples of rebels and sinners who grumbled, killed, rebelled and gave false testimony (Cain, Balaam, Korah)
…They are clouds without rain, blown along by the wind; autumn trees, without fruit and uprooted—twice dead. They are wild waves of the sea, foaming up their shame; wandering stars, for whom blackest darkness has been reserved forever. Jude 12-13
            First, Jude tells us to understand that these rebels are spiritually dead and shameful.  Be sad for them first.
Enoch, the seventh from Adam, prophesied about them: “See, the Lord is coming with thousands upon thousands of his holy ones to judge everyone, and to convict all of them of all the ungodly acts they have committed in their ungodliness, and of all the defiant words ungodly sinners have spoken against him.”  Jude 14-15
            Second, know they will face judgment by God so it’s not your job to force them to face judgment.
These people are grumblers and faultfinders; they follow their own evil desires; they boast about themselves and flatter others for their own advantage…They said to you, “In the last times there will be scoffers who will follow their own ungodly desires.” These are the people who divide you, who follow mere natural instincts and do not have the Spirit.  Jude 16,18-19
            Third, know that they don’t know what they are doing.  They operate off selfish instinct because they don’t really know God.
Be merciful to those who doubt; save others by snatching them from the fire; to others show mercy, mixed with fear—hating even the clothing stained by corrupted flesh.  Jude 22-23
            Finally, be merciful and work hard to save them from eternal separation from God.  Hate the sin (the outward clothing that’s corrupted by flesh) but love the sinner (the inward person who is lost and far from God).