If you pay taxes to the federal government are you complicit with all of the government's actions? Well sure, but what other option do you have? You could not pay taxes and go to jail, or you could move somewhere else where there isn't an imperfect government--- say Antarctica.
Similarly, what are you going to do if you decide not to work for some "complicit" organization? Move to Silicon Valley and work at a startup? Is that any better? Is there any company that is morally and ethically perfect?
Governments, industries, populations, etc. are all part of an inter-related system called The World. If you think this system is imperfect and should be improved, then exiting the system won't solve anything. Rather, you can work within the system and do what you can to make it better.