How do I keep my conscience separate from my company?

You can steer a company through any storm. That skill made you valuable, and it slowly pulled you into speaking the company's line so often that you lost the seam between its interests and your own sense of right. That blur troubles you, which means your conscience is still alive under it. The company's line is a role you play, not the whole of who you are. A role can be worn without being swallowed, but only if you keep a private place where you judge things by your own standard, not the company's. When you cannot tell the difference anymore, it is because you stopped checking in with that private place. Before the next statement you defend, ask yourself quietly whether you actually believe it is right. You do not have to quit over every answer. But naming the gap keeps it from closing. The line you will not cross is yours to decide, and deciding it is how you get yourself back.