A properly functioning complex system should be able to tolerate a few bad apples, limiting the harm that they can cause. If you work in such a system and there are bad apples, you can justify the ethics of your work if there are checks and balances that limit the leader's ability to harm.

The obvious analogy is the current U.S. political system. It's quite possible to see the United States as generally striving for a more fair society, and generally good, and yet to be disgusted by Trump's cruelty and inept. The only way to square those two competing ideas is to acknowledge that even though Trump is a miserable rotten apple, he doesn't really have all the power. As bad as he is, he won't last forever, and the principals of the U.S. will long survive him.