The short answer is Yes virtually all of the Jim Crow laws were rooted in religion.

The longer is answer is yes but they were pretty shallow and cherry picked and all politics at that time would have been steeped in religious imagery. If you needed to pass a bond to build a new sewer you would invoke the almighty in an attempt to get it passed or defeated depending on your views on sewage.

Bob Jones Sr. founder of his eponymous university gave a famous radio sermon outlining one of the positions:

Yes, Paul said, “God… hath made of one blood all nations of men…” All men, to whatever race they may belong, have immortal souls; but all men have mortal bodies, and God fixes the boundaries of the races of the world. Let me repeat that it is no accident that most Chinese live in China. It is not an accident that most Japanese live in Japan; and the Africans should have been left in Africa, and the Gospel should have been taken to them as God commanded His people to do.

Wherever we have the races mixed up in large numbers, we have trouble. They have trouble in New York. They have trouble in San Francisco. They have had trouble all over California. . . .

Let me tell you something. When it comes to the quality of races, all these races have quality. They have good qualities and bad qualities.

If we would just listen to the Word of God and not try to overthrow God’s established order, we would not have any trouble. God never meant for American to be a melting pot to rub out the line between the nations. That was not God’s purpose for this nation. When someone goes to overthrowing His established order and goes around preaching pious sermons about it, that makes me sick – for a man to stand up and preach pious sermons in this country and talk about rubbing out the line between the races – I say it makes me sick. I have had the sweetest fellowship with colored Christians, with yellow Christians, with red Christians, with all sorts of Christians – the sweetest fellowship anybody has ever had, we have had. Christians have always had it. We have never had any trouble about that.

The trouble today is a Satanic agitation striking back at God’s established order. That is what is making trouble for us.

Basically God's established order. I love Negroes as Christ loves you, I just don't want the filthy animals anywhere near me or my family. You know, common sense.

Another major factor was 'purity' this is a bit more amorphous and not necessarily a religious justification as it is a cultural justification steeped in religious ideals of sanctity and holiness confused with racial identity.

UNC–Chapel Hill Professor Emeritus Donald G. Mathews writes in the Journal of Southern Religion (copied from Slate.com):

Religion permeated communal lynching because the act occurred within the context of a sacred order designed to sustain holiness.” The “sacred order” was white supremacy and the “holiness” was white virtue.

Now, Judge Bazile in 1959 had a case that would eventually become Loving v Virginia. When he decided it he said:

“Almighty God created the races white, black, yellow, malay and red, and he placed them on separate continents. And but for the interference with his arrangement there would be no cause for such marriages. The fact that he separated the races shows that he did not intend for the races to mix.”

Theodore Bilbo, US SENATOR BILBO (of MS but still) said:

[p]urity of race is a gift of God . . . . And God, in his infinite wisdom, has so ordained it that when man destroys his racial purity, it can never be redeemed.” Allowing “the blood of the races [to] mix,” according to Bilbo, was a direct attack on the “Divine plan of God.” There “is every reason to believe that miscengenation and amalgamation are sins of man in direct defiance to the will of God.”

They don't hold up well but there they are. Basically amorphous 'purity' talk and a reverence for the status quo..