Who says we're absolving the members of the employees? If you continue to strip away the abstractions, an evil person is just a collection of neurons and other cells that are collectively making decisions to hurt others, but it's still reasonable to call the person evil. Likewise I would argue that we can call a company "evil" if the people who make it up are acting in an evil way.
People absolve the companies all the time. "They're just employees, they don't make the policies." "Oh, yeah, Zynga's awful, but he's a good guy." Etc, etc.
I think that's factually true, but the moral implication is false. Nobody says, "Oh, it's not his fault the mob assigned him to break kneecaps. He doesn't set the policies, you know."