Trek has always avoided this good guys vs. bad guys simplicity. I don't wanna imply moral relativism, there is good and evil in the work and most of the times it is clearly recognizable from an objective point of view. But when we have to make decisions it can become very difficult to avoid the temptation to do something wicked.
So there aren't good guys and bad guys (I have done good and evil things in my life but I am neither a good nor an evil person precisely because I am free to do good or evil and not condemned to always be evil or blessed to always be good) but there is good and evil and all of us have to continually struggle to do good.
If this sounds slightly Christian it is not coincidental, it is after all Christmas. I stick to the words written by my favourite Catholic author who has ironically often been accused of portraying a simplified good vs. evil story (usually by dumba*ses who never read his work) :
Many that live deserve death. And some that die deserve life. Can you give it to them? Then do not be too eager to deal out death in judgement. For even the very wise cannot see all ends.