The emergence of the idea [not a concept] of God arose within human consciousness because of a psychological impulse to counter a very terrible existential crisis inherent and unavoidable within the human psyche.
As Kant wrote [mine];
The idea of God arose out of desperate psychological reasons but nevertheless such an idea [philosophical] is based on reason and logic [attempted] but it is primal pure reason similarly to those used by the ‘higher’ beasts [primates, etc.].
The idea of God started with crude reasonings but nevertheless are countered by non-theists and others which set forth a spiral of arguments and counter-arguments which end up with claims of the tri-omnis and whatever ‘omni’. Because of the desperation based on crude reasonings, the refiner consideration of contradictions [as in the example you raised above and others] are missed out.
In facing more counters from non-theists, theists has to push their claims to the ultimate ontological God, i.e. an Absolutely Perfect Being. With this, God can do no wrongs, because whatever contradictions raised God being perfect has the perfect answer to it but humans being imperfect and infallible will not be above to understand God.
However, when theists pushed their God to the ultimate as an ontological God, they are actually setting themselves for the final checkmate move against themselves.
When they pushed their God to the level of the ‘absolute’ thence ‘Absolute’, i.e.
“If the term absolute is understood in the strict sense, it rejects the relativity which is inherent to the mechanism of human cognition, understanding, and language.”
http://www.newworldencyclopedia.org/entry/Absolute_(philosophy)#Conceptual_issues
it transcend beyond to the ream of the empirically impossible.
Thus God cannot be … i.e. impossible to be within empirical-rational reality.
Theist: I will kill you because you are a non-theist as God sanction it and said so in the holy text God delivered through his messenger.
This is what is really going on at present because the majority accept God as “really real” thus providing ambient support to all theists including the evil prone ones.
Since the idea of God began from the psychological, the only solution to all questions and evils [such as the above] associated with God has to be resolved from the psychological basis.