A lot of people like to take a crap on modern society for things that occur nowadays that they consider inhumane, but I honestly believe that the governments of today are infinitely more humane and reasonable than what existed 500 years ago. Humankind has moved away from tyranny, despotism, and incivility to a large degree, because our history is one of freedom universally benefiting our species. Consider how easily an intelligent species in more dire situations could adopt an antithetical view to our "freedom and democracy are good" concepts, and you begin to see that aliens, though advanced, could still be quite barbaric and frightening. Two quick video game examples:
Fallout New Vegas, Caeser's Legion
There's some brilliant political commentary on the efficacy of Democracy in survival situations here. What seems horrible and savage can fulfill a purpose of bringing about order in times of anarchy. Sometimes the ends do justify the means, thinking that isn't ever true is a luxury of comfortable society.
And two cases from Mass Effect 2
1) The Quarians
A species that literally exiled itself through slavery of intelligent technology that backfired. They literally have no home world to call their own now. They wander the galaxy bent on reclaiming they planet they evolved on through any means necessary since it is the only place they are evolutionary adapted to exist on. They can't settle somewhere else because their physiology is incapable of surviving there, yet getting what they want means genocide of an artificially intelligent race -- and do they even deserve moral consideration because they are artificial?
2) Racial superiority
When you encounter different intelligent species, some of them actually will quite literally be genetically superior. This isn't something humans have actually dealt with because we're all roughly the same genetically, but imagine how a galactic civilization would cope with actual, tangible inequality? Do inferior beings deserve equal consideration? Should species genetically modify themselves to be in line with the top-tier species?
My point with these science fiction examples is that aliens, were they to exist, would live in such incredibly different circumstances. Their perspectives and priorities would be so different from ours and they would represent a million moral and technological quandaries that we've yet to encounter. All of the speculation about their existence, and the desire for them to exist, misses this point.