Very many were, that is true. However, very many fought as soldiers. They fought like hell and killed many a Union invader. Northern Republicans and Union army veterans testify to that truth.
...And that that the idea of facing armed black men in combat, as equals, was totally foreign to the average confederate soldier and that was what they found horrifying?
Nah. My previous explanation is the correct one. That feeling of betrayal and the outrage born of it was expressed in many diaries and letters of the time.
Then why was Robert Lee saying as late as January 1865 how he would have preferred to fight with a white army? Especially if his command had been integrated for some time.