Recently I've been listening to a Civil War podcast, and I've been surprised (though I shouldn't be) of how extremely racist a lot of the political rhetoric was prior to the Civil War in the arguments for slavery.
Most of the arguments were based on the supposed scientific "fact" that the whites were a genetically superior race, and were given dominance over the world, whereas blacks were an inferior race, given to serve the whites and to be passive.
Being an Eastern Orthodox Christian, most of our church's Saints, as well as many adherents of the Oriental & Eastern Orthodox churches, such as those in Greece, Syria, Lebanon, Israel, Egypt, Ethiopia etc... are all of a much darker skin-tone than Western Europeans.
The fact that many, if not most Biblical figures, including Christ and the Apostles, would have had a darker, olive toned skin color is seemingly very apparent. It absolutely astonishes me that many Americans at the time, of mostly Protestant background (and therefore many knew their scriptures back to front) would have a weird, overtly racist viewpoint that whites were inherently dominant over blacks.
Based on writings from the time, did white Americans ever realize that their God (Jesus Christ), and other figures like his Mother and the Apostles, would have all been darker skinned with black hair?
Or was this something they wouldn't have considered at the time, or would have been ignorant of? Or did they just assume that Jesus & Biblical figures must have looked like them?
Also, how did they reconcile the fact that many whites were enslaved in other parts of the world, and that it wasn't just blacks who were?
Not a direct answer but there was a Jewish population in the antebellum and confederate south. The Confederate secretary of state was a Jewish - American Judah P. Benjamin. There wasn't the same level of anti-semitism as there was racism. The bible itself was also construed as justifying and explaining slavery in the south as well.
I'm not sure whether this was the case during the Civil War, but certainly during the late 19th Century/early 20th century, there were certain racial where some Africans would not have been considered 'negroes'. The standard races of the world at the time were 'Caucasoid' ('white' people), 'Mongoloid' (East Asians) and 'Negroid' (blacks), but the 'Caucasoid' race would have been divided into 'Aryans' (people from Europe, as well as Iran/N India), 'Semites' (Middle Easterners) and 'Hamites' (people from the Horn of Africa). Often the boundary between 'Hamite' and 'Negroid' was quite arbitrary, however, so it is quite likely that Americans in those days would have justified their racism by saying that Nubians/Ethiopians weren't black people, but Hamites, who were Caucasoid and therefore superior to blacks. The same would apply to most of the peoples in the Bible, who would have been regarded as Semites, and therefore superior to blacks.
tl;dr, racial hierarchies in those days didn't just consist of 'white Europeans' and 'everyone else', they were considerably more complicated than that.
Having said all that, you might want to look at how slavery was justified by the Curse of Ham. A similar argument was also used in South Africa to justify Apartheid.