I see that you're having difficulty putting this into perspective. In your place of work, do you not stand up for what you believe in? Do you not professionally challenge your superiors? If not, that's an unhealthy work environment.
I guess I'm lucky. Where I work, if I disagree with something, I'm comfortable saying so. Your definition of "acting professionally," appears to be silently taking orders, whether you agree with them or not. To me, that's weak, I'm sorry.