First of all, I would like to argue that morality does not "automatically" arise when we reach certain level of intelligence. Morality is a social construct, having certain level(and/or beyond) of intelligence could help in developing moral concepts/theories. So, by saying that Reapers are intelligent does not automatically make them moral(perhaps they deem morality as something that ought to be abandoned, useless in their society, if Reapers have one AND is like ours).
Secondly, "empathy" is a kind of emotion. You "feel" empathy toward other humans or life form. However, you do not "THINK(as intelligence means the ability to comprehend/interpret information coming from both external and within)" empathy toward other humans or life form. The question rests on can you give a valid argument that the rationale of empathy IS intelligence. Here I would assume that intelligence is mainly rooted in logic(personally believe that it is rooted in logic and nothing else).
As far as Geth is concerned. I would use the Chinese room thought experiment. Here I will just give a concise version of what it entails..."a computer can never be properly described as having a "mind" or "
understanding", regardless of how intelligently it may behave." Geth may be incredibily efficient at processing information and output appropriate response. But does that mean that they "THINK" or have "MENTAL STATES/PROCESSES" like us? Personally I think not. Then again, this IS a subject of dispute in the area of AI and philosophy of mind.
And to your last query...what "EVIL" are you speaking of. EVIL in terms of human perspectives? Unless you believe there is OBJECTIVE "evil". Then I have to ask, what is THAT? If there is NO objective evil, then because what you see as evil does not mean that it REALLY is. After all, as you pointed out yourself, the Reapers are "vastly more intelligent". So, why is not a possibility that at their LEVEL of thinking, what they do seems totally reasonable and even possibly MORAL to them?