Do you believe that the German people in 1933-1945 were all (or many millions of them) mass murderers and "evil"? The reality of it is that they just followed orders, and that doing a little part doesn't directly feel like being a murderer, especially if its celebrated by your peers and superiors. The "banality of evil" and all.
But in the case we're talking about it's even easier. For one, it doesn't have to be "many thousands of people" working in the company. Just a few, entrusted by the upper echelons. In the same way that companies historically employed thugs, mafia etc, to beat and even murder union members and strikers. It's not like it was something openly decided in a company meeting. Usually it takes the form "take care of the problem, the less I know the better" from some superiors (with an implicit knowledge of what that entails).