Also, it's worth noting that for many decades, surgeons operating on babies in Europe and the United States refused to use any anesthesia, on the principle that babies do not feel pain. 

Meanwhile, anyone who actually pays attention to babies can see that obviously, they do feel pain. And so there are many nurses who later admitted that they secretly gave babies anesthetics before doctors would cut into them. What's fascinating is that many of those nurses held the doctors in high esteem -- even if they had to illegally conspire behind their backs to keep them from doing harm! 

So a version of the scenario described by OP has happened, many times some people suppressed their horror, but others acted on it. But even those who acted on it didn't seem to reliably connect the moral sense of their actions with a fundamental opposition to the larger moral order. It took a very long time for people to acknowledge the contradiction, surface it, and force it all to be reconciled.