I feel like you are misrepresenting the quest. The ebon emperor is evil. The fact that he is currently in need of rescue is beside the point. No matter what our me thinks the rest of the world will see bringing him back as an evil act.
Besides, the nature of good and evil is beside my point. It seems like every quest on this site people try to turn into a pacifistic diplomatic adventure with a happy ending.
Just once I want a quest where we fight the war instead. And here we have the perfect chance a villain quest where are power is explicitly "create dark army" and our goal is "create dark empire to revive dark god" yet you are still trying to twist it into a hero quest where we can make everyone happy.
Just once I want evil to win. And I will be severely disappointed if our am actually lets us convince everyone that reviving a dark god is somehow a good thing.
I believe you are misreading my argument as well, but... well, whatever.
In all honesty, I could not care less whether Jacob is good or evil. What I do not want to see is being evil just for the heck of it; our protagonist was established as not being a sociopath, so this kind of behaviour would make no sense.
What I hope to get from this is an interesting story that examines the concepts at work, nothing more and nothing less. The premise we are given is what it is, so there can be nothing done about it.
Additionally... this may just be my interpretation, but... what does it matter?
Jacob has vowed to save the Ebon Emperor; I looked over our traits a few minutes ago, they include the former as well as the trait Driven. If we have to be 'evil' to do so properly, so be it. If doing this by moving through the different layers is more useful, so be it.
If being good or pacifistic or whatever is the best course of action, so be it. I personally do not care, for as long as we do not do something just for the sake of doing it.
If I made it sound as if I thought that the Ebon Emperor was a good guy all along or something like that, I apologise; that was not my intention. However, people can change... and unless I am disproven by canon, I will continue to believe that the eons of being sealed away changed this being we are going to free; be it for better or worse.
Either way, I guess we have to agree to disagree; this discussion is fairly pointless for both sides, I guess... feel free to put up another statement to this to wrap things up, but please do not push this any further. We would only be going in circles.