While a perfectly moral person would prefer to die instead of compromising their ideals, people are not perfect, and we are wired for survival, so I concur.
I can name two reasons. For one, I like to look for best practices for guidance. Second, if I think one way and find that lots of people think otherwise, that might be worth investigating why. I might learn something.
The good thing is that I'm exactly as free to discard everything, and just go my way, as I was before. But at least I made an informed decision.
Working for a company that creates life-saving vaccines, or builds homes for underprivileged people, or increases yields of crops to match the demands of a growing population doesn't make you a good person? Well, how high is your threshold then?
I don't think that the work you do should be the only thing that defines what type of person you are. Someone could work at those types of companies and be a serial killer in their free time.
The perspective of what good and bad is, is very subjective.
Making weapons = bad
Making anthrax = bad
Making weapons which kill your enemy (aka the one trying to kill you), which are more effective, could actually = a less bad company. If you are a patriot, then working for a company like Lockheed Martin may be seen in your own eyes as good. Same with FB, it is connecting the world (Trademark Zuck).
Coal Power is bad, for the environment but it is good for society as we need electricity.
So there are two perspectives to this, how you judge yourself and how others judge you. The internal is based on your own views, and the external is based on 7+ billion views and there will always be conflict in both.
So to answer your question
> Who decides what 'bad' is?
Everyone and no one. It is a paradox, and the original `No` answer to this question would be simplistic and out of touch with reality. The better question is, if I know the company I am working for is against my moral, ethics then does that make me bad?
Even when I worked for a large defense company which built systems to kill people at war, there were good aspects of it. There was one group that was building systems to monitor the rainforest. Another group was supporting the antarctic scientific missions.
There are also people that work to change the organization from the inside out. To be honest, if you want to change corporate culture, that's how it has to be done.
As an atheist, my line between bad and good is "don't harm others". Ideally, those others include living beings besides humans, but ffs, if at least you restrict to humans, even if you never actively help anyone, it's a great improvement.
So we would have to ask: do I harm others by working for this bad company?