Not in Mill's conception - an omnipotent God cannot be "forced" into choices or trade-offs, not even temporarily. Whatever that greater good is, an omnipotent God had the power to achieve it without tolerating evil, but for some reason chose not to.
That's hardly fair -- especially to someone so good, powerful... and so very authoritative to boot.
Perhaps. But then again, it didn't have to be that way if He is truly omnipotent ;)
This of course, assumes control, not allowance of moral self-control by free beings. Isn't the former inherently "good?" Be careful now, the answer to that question will decide whether or not one is a classic libertarian! Sounds like Mills would be fit for DU.
So I do not think it is at all fallacious to say that the creation of free moral agents is not good. And, if God chooses to withdraw some of his control, in order to do so, that is the act of one yet omnipotent.