Is there a parallel of evil between "In the Penal Colony" and O'Connor's "A Good Man is Hard to Find"?
The evil that is presented in each story is an impersonal evil.
The officer in Kafka's story, "In the Penal Colony", has nothing personal against the condemned man. Instead, his passion and his angst have their source in the bureaucratic regime in which the officer is a functionary. The officer is not exactly a tool of the system, but his tension is thoroughly connected to his views of the system of which he is a part.
Willing to put a man to death for falling asleep on duty - and willing also to condemn the man without a trial - the officer is an absolutist without any moral compunction. He articulates his views at one point in this way:
"My guiding principle is this: Guilt is never to be doubted."
In O'Connor's story, "A Good Man is Hard to Find", evil is equally impersonal. The Misfit holds also to a rather absolute theoretical "moral" framework, basing his ideas on a particular view of the New Testament.
The Misfit explains that "Jesus thown everything off balance."
He will do what he does, acting out of an evil intent, regardless of circumstance. He is not angry with the family, but he kills them all (or has them killed) anyway.
Each of these characters then can be seen to hold to moral frameworks that lead to callous and immoral behavior. These frameworks serve to justify evil and this evil is not directed against anyone in particular.