I can't answer the question since I live by different principles, but I'll try to help you anyway.
and possibly loose everything in the process (my job, my acceptance in society, my life etc).
First of all that's just fear in your head, and I believe most of those things wouldn't happen.
Would you work in a job where you would be required to lie from time to time?
No, since I live by the principle of Truth.
Would you work for a pharmaceutical company knowing that ONE of their products actually had more negative effects, and the management knew it?
Again no, since I believe that it is very important to provide value, which is always in high demand.
If not, what exactly would you do? Would you quit right away, regardless of the effect of this decision on your career and life?
Absolutely not. I'd wait until I'd be ready since it's not smart to take on too big risks.
Would you work for a company that tortures animals somewhere along the production chain?
No, I live by the principle of Love.
If in a job you loved, you were given ONE assignment that required you to harm or deceive someone, in any way, would you do it? Or would you refuse, even if that would get you fired?
No, because I believe that isn't so selfish at all, especially if I'd love the job, since working on yourself is a really selfless thing to do.
Would you ever do something you considered wrong, because you believed that the positive effects would outweigh the damage? Would you condone lying, incarceration of innocent people, torture, killings, if you were absolutely convinced that from a rational, political point of view, your actions would be absolutely necessary for the greater good?
I don't believe that torture and killings are for the greater good.
How would you handle not being able to understand how your decisions or actions will affect a group of people or the country as a whole?
Would you feel comfortable deciding the DEGREE to which individual freedom should be sacrificed for security?
I don't live in America, so I don't understand your whole freedom thing.
Would you accept to be a soldier if your country attacked another? How about if it was under attack?
Neither.
Would you kill enemy soldiers who you knew were just following orders? If not, would you just let yourself be killed or sentenced to jail for that, with no hesitation?
I wouldn't kill them even if they weren't following others(i.e. generals,...). I wouldn't have to get a sentence to jail since I wouldn't apply to army in the first place. And no, I wouldn't let myself be killed with no hesitation. But going to army wouldn't decrease the risk of getting killed, would it? In fact, it could only increase it.
What would you do as a political leader? Would you condone war for any reasons? If not, what would you do?
I would not support war. I don't know exactly what I would do, but I believe ways of peace would presented to me by the universe.
How would you feel about paying your taxes if there were some policies that you didn't agree with?
I'd just pay the taxes. No need to fight the system. It's much better if you try to change the ones controling it.
How is integrity compatible with supporting a government that (among many positive things), also condones some negative ones, such as a war in some part of the globe? This applies only if you are in fact totally opposed to war.
I don't think a goverment would condone many positive things if it condoned war.
What if some sort of authority wrongfully denied you your freedom, in a way you would consider truly wrong?
I would not fight it.
Would you allow someone else to keep you captive and lead you around, or would you be ready to fight against anyone who imposes domination and torture upon you?
I don't believe I'll be in such a situation any time soon. But I think if it was no big deal I would fight it. If it was keeping in me in jail or in real torture, there probably wouldn't be much chance to resist, would there be? I'm not some John Wayne, or Sam Fisher if you're into games.
What if your actual captors were just following orders from superiors?
Same as above.
If someone you cared about was in this situation, would you try (and risk) anything in order to save them?
Same as above.
In conclusion, always remember that you are not going to die,
so just relax a little bit. Just don't fight the system, but try to change yourself and others. Also, I hope that I helped you with my effort.