An intriguing argument indeed.
Some thoughts.
"If God did not create moral standards by command alone, then those moral standards must exist apart from God."
Insofar as we take 'God' to be a reality, moral standards cannot logically exist apart from God. Firstly, moral standards cease to exist when the relational context - 1.God and the 2.entity on whom its 3.morality is imposed - on which it depends on for its existence, ceases to exist. What is 'good' assumes a context within which it can exist as such, even though 'arbitrary'. The subtraction of either 'God' or the 'entity'(humanity) from this relational context renders the idea of 'moral standards' superfluous.
When the existence of 'God' is taken to be true, then the existence of moral standards apart from God assumes that the former exists despite God which in turn negates the idea of a God that is omni###.
"Are morally good acts willed by God because they are morally good, or are they morally good because God commands them to be?"
If God is taken to be the 'Ultimate Good', regardless of our understanding what this 'good' is in its entirety at any particular point in time, then one can view the Laws emanating from God as, analogusly, the 'word made flesh' (or vice versa). If God wills atrocities, then God logically ceases to be the 'Ultimate Good'. The dillema posed by the aforementioned question is derived from the structure of the question which presents two alternatives as if there are none other. For instance, the question could be structured as such :
"Are morally good acts willed by God because they are morally good, or are they morally good because God commands them to be, or, are they morally good because they are willed by a morally good God?"
The first question is based on an assumption that God is capable of willing that which is not 'morally good'. The second assumes the value of omnipotence in defining that which is 'morally good'. The third considers the possibility of a God that issues moral standards from the fount of its omnibenevolence.
"If said God were omnipotent, omniscient and omnibenevolent, then that God must logically be dedicated to disallowing any atrocities from happening. "
If God is taken to be a real entity capable of exerting power, then its omnibenevolence called into question by its failure to assert omnipotence in the event of 'evil' is acquitted by its omniscience. (insofar as 'omni' here refers to being unlimited in ways that humanity is.)


And, even if it were Jesus, this literally means nothing.. half of the things we experience today are directly traced to someone who was historically insignificant in their own era. It's called complexity, not God.
