Will Atheists be Targeted as "The Anti-Christ"?
No need to "target" them alone:
"and every spirit that does not confess Jesus is not from God; this is the spirit of the antichrist, of which you have heard that it is coming, and now it is already in the world." -1 John 4:3
"For many deceivers have gone out into the world, those who do not acknowledge Jesus Christ as coming in the flesh This is the deceiver and the antichrist." -2 John 1:7
"Who is the liar but the one who denies that Jesus is the Christ? This is the antichrist, the one who denies the Father and the Son." -1 John 2:22
"Children, it is the last hour; and just as you heard that antichrist is coming, even now many antichrists have appeared; from this we know that it is the last hour." -1 John 2:18
Atheists, then, are antichrists. However, they alone are not the only antichrists. Anyone who denies that Jesus Christ was a real, historical, being, who dwelt within a fleshly body, the messiah, the son of God is an antichrist. Anyone who denies the Father, God, is an antichrist.
Will lack of religious affiliation with a church be the determining factor in declaring one as an "anti-christ"?
No, see above.
If you are not a baptised, signed up, tithing church member somewhere....will this be the dividing line?
No again, see scriptures above.
Will church membership be the sole criteria of "godliness" in this battle of Armageddon?
Ditto.
Who gets killed off .....the good moral atheists or the hypocritical self righteous christians?
That is up to Christ. (Matthew 7:1; Luke 6:37; Hebrews 4:13; 1 Timothy 2:4; 1 Peter 4:5)
BA- Search the Scriptures for answers.