Take Adam and Eve, for example, to give us the feeling that we are all brothers and sisters. Or the Fall, supposed to teach us to work towards God because we are in an ignorant state. It is not logic, so much, that is being used, to teach these things. Traditional logic gets in the way of wisdom.
Maybe the question to be asking is "why" instead of "how". Why did God want the Israelites killing all their enemies? Because it got rid of tainted influences. Well, that's wrong of God, some say. It depends on how it's looked at. If the enemy really is doing the wrong thing, well, then it's only one generation of evil if we kill them, as opposed to generations of evil if we don't, as well as the risk that their evil will totally nullify the truth of the Israelites. This isn't a question of God letting choice exists, because He does. It's about consequences for your choices. The enemy was living in evil, therefore this is how God punishes evil. It's not that I condone this sort of thing, but the logic is there if you take the time.
Perhaps an even better question would be why is this evil, while another thing is good? Why is it that enlightenment must be attained, or attained through only certain methods? Why can't it be good, then, to be evil, and vice versa? Couldn't we get the same results if God merely desired it so? Couldn't God snap His fingers and we have all the wisdom we would need to fully appreciate good? But perhaps that negates true choice, in that how can we make the choice without the question being posed as it currently is? But, again, couldn't God merely desire it so, again, to make us fully aware?
These are the type of questions that I would expect to hear from somebody truly questioning and searching for enlightenment, instead of focusing on another's beliefs. What is being accomplished by tearing another person down, of telling them that they are wrong, making them feel like they're inferior, questioning their logic instead of finding your own, etc? I have a hard time believing it is enlightenment that has such anger and hatred, and even joy of the woes of an organized religion or of your own enlightenment compared to their ignorance. When I see pride stemming from another's perceived ignorance, it always make me question the motives. Who is to say you haven't gotten it wrong? You believe in your truth, as much as they believe in theirs. Logic doesn't make something true or not, because it's a lot deeper than that.
A big part of the Jesus story was that, yes, humanity is an ignorant bunch, but that doesn't make God love you any less, or not provide the means to get to Heaven. You can be as wrong as you are, but, if your heart is in the right and good place, then there's a shot. Hey, it may not be the truth, per se, but the message is still intact.
* When we start identifying wisdom with our ability to comprehend its form, what wisdom is that?
* Judge not, that ye be not judged. For with what judgment ye judge, ye shall be judged: and with what measure ye mete, it shall be measured to you again.
* People want platitudes, not progress.