I thought that while I'm active on the board again, I'd take a stab at a personal answer to the question you posed last fall. As it is a personal answer borne out of my own experiences, it may not be that meaningful to you, yet someone may find it of interest at some point.
The simple answer why such things don't bother me is that's I'm not a member of any of those religions, and I don't view myself as entirely human [link], so from my POV it is rather like studying any other species which may have disagreeable aspects (c.f. Yersinia pestis). A deeper answer, though, is that many of the purported "commands from God" in those ancient documents strike my pattern recognition talent as being entirely human justifications for behavior, and do not proceed from non-human entities at all. The ones that don't fit the human-generated pattern are demonstrably odd enough to have a non human origin. God's "I am that I am: thou shalt say "I am" has sent you unto Pharaoh." is one example. It just isn't something a human would naturally say. With the Gospel of Thomas, such sayings are much denser: in effect, Jesus talks like a Salvia-person. Examples: "Jesus said, "If your leaders say to you, 'Look, the (Father's) kingdom is in the sky,' then the birds of the sky will precede you. If they say to you, 'It is in the sea,' then the fish will precede you. Rather, the (Father's) kingdom is within you and it is outside you." and "Jesus said, "The person old in days won't hesitate to ask a little child seven days old about the place of life, and that person will live. For many of the first will be last, and will become a single one."
Now, this method is probably not generalizable, and thus of little practical utility to the general reader, yet that is my technique for what it's worth.