There are three pre-analytical observations that I need to make before I began rambling through the various issues:
One. In the final analysis, we may not have an answer to the (second) question "why?", which means that we will not be warranted in answering it negatively or positively. If we are not able to discover a motive for God's decision to 'go ahead anyway', then we will not be justified in judging that unknown motive to be either adequately good (to warrant a positive 'assessment' of God's character) or to be insufficient (allowing a 'worse-than-us' value judgment of God's heart).
We must be clear on this. Absence of data on "the motive" will not allow us to assume that the motive is inadequate to "justify" the choice to "go ahead". We will not be able to jump from "ignorance" to "certitude" with any level of warrant. Methodologically, it would be just as inappropriate to assume God's guilt (given this absence of data) as it would be to assume God's innocence in the matter. The Christian may be warranted in extrapolating from instances of God's alleged grace, goodness, and kindness elsewhere to this issue, and the skeptic may be warranted in extrapolating from instances of God's alleged cruelty and insensitivity to this issue, but we must be clear that this is pure extrapolation and extension, and cannot carry nearly the same force as the content of the motive itself.
Two. We must note that, in the first question, we (somewhat insignificant 'carbon-based life forms') are presuming to judge God's morality and character on the basis of our own! For a human being, with the incredible paucity of data we have about the universe, morality, reality, and complexity, to decide that God is less kind, less noble, less compassionate, less moral, less 'humane' than they, seems quite bizarre, in my opinion.
Think about this for a second. Let's consider two cases: one without a God (i.e., Materialism of one form or another) and one with.
In the latter case, we have a God that somehow creates a derivative, "smaller" creature (i.e., human) with a superior morality and better heart! So, when a person says "I refuse to worship such a heartless god" we have the absurdly strange situation in which the "effect" is somehow greater than/superior to the "cause". [If you haven't read Aristotle recently, perhaps now is a good time to read his discussion on causality, to see what problems this might include (sardonic smile).] This is pure and naïve presumption...[Notice that the analog of this--"I have a greater intelligence than the absolute source of all intelligence" makes the absurdity even clearer.]
In the former case of materialism (no spirits or deities or 'souls'), we have a creature that has climbed from the slime to some kind of superiority (i.e., "top of the food chain"!) by wholesale application of 'survival of the fittest' (read: "extinguishing" or "subjugating" others). Vast amounts of human evil--the responsibility for which is borne in this scenario solely by the human, since there are no other agents to pin this on or share the blame with--have been perpetrated and are inexorably justified, under the evolutionary leveling of all to 'self-interest'. The elimination of countless species of life in this evolutionary, ceaseless, and random struggle; the very atrocities that are used as examples of 'the problem of evil'(!); and the wholesale failure of the human race to produce anything in the area of human rights at all but the most insignificant scale, makes me question the 'moral superiority' of such a creature...Indeed, since his moral judgments will eventually reduce to thinly-disguised but cosmetically-complex positions of 'self-interest', why should they be taken as 'objective' in any sense? Despite Herculean efforts to construct systems of evolutionary ethics to account for altruism, cooperation, and "animal rights" type of oddities, while attempting to avoid the racist and biological supremacist implications of the early Darwinian exponents, we are stuck with our own bloody and shameful history of action. [Recent studies on advanced forms of cooperation in higher primates(cf. PH:GN) only pushes the problem 'down' and 'early' a little further.]
To agree that a "mudball, with hair and teeth, red in tooth and fang" can transcend this history to the point of making authoritative statements about morality and character, is well beyond my skeptical limits...
The very fact that I believe that I can make moral judgements about my actions and the actions of others, presuppose that my source of origin has at least as good an ethical standard as I. For me to believe that I can make objective moral judgments, and then take the position that my ontological source of ethical abilities is inferior to me, borders on the self-stultifying. [This is not to mention the problem of the Ultimate Reference Point of morality, as noted by the Existentialists. There has to be a "God the Father" for real value to exist, to use Sartre's explication.]
Now, strictly speaking, the skeptic is certainly warranted in raising the question of God's character--on the basis of his individual exegetical and theological construction--I would not fault him in the least for this. We often do this; something strikes us morally 'odd' about a passage or a doctrine, and it forces us to examine it more closely and more carefully and more open-mindedly. Often in the this process we discover our 'hidden baggage' that we bring to the text. In the skeptic's case, however, instead of having an independent basis (such as a warm personal experience of God or a careful and informed understanding of the life and character of Jesus Christ) for giving God the "benefit of the doubt" and suspending judgment until he has time to turn all the possible understandings over, he instead hits the "Finish" button and arrives at the conclusion.
The main problem is one of sequence. The skeptic foregoes deciding about the more 'objective' issues such as "was prophecy fulfilled beyond reasonable plausibility?" or "did the resurrection really occur?", or "how did Jesus feel about this God?", and instead starts the process with a subjective moral judgement of God's character, based on his fundamentalist-like understanding of Genesis and some of the other texts (some of the stranger texts in the bible, I might add). In normal life, one generally tries to move in the opposite direction--from the more-sure to the more-questionable...
Three. This objection sounds strangely like the one advanced by the famous serpent in the very passage under discussion. The serpent in Genesis 2-3 advances two propositions: (1) God is a liar; and (2) God does not desire your best, and His motives cannot accordingly be trusted.
Notice that this 'objection' (at least as worded in most forms) intends the same result. It attempts to get us to say that (1) God is a liar [i.e., He is NOT good, merciful, kind, benevolent, and interested in the welfare of all His creatures, great and small, in spite of all the statements and evidences He adduces to this effect); and (2) God does not desire our best (but His own best) and His motives cannot be trusted. I find this diabolically ironic that the passage describing the first 'attack' on the beauty of God's heart is used so effectively in our time to do exactly the same!
Although this, of course, cannot be used as evidence against the position itself, the similarities might suggest ways of approaching the question.