I speak as a categorical nonbeliever in, sometime practitioner of, lifetime thinker about, religion. I take no exception to any of your examples of bigotry in religion. But I also recognize that these bad ideas are not the only ones religion has to offer. The fault lies in failing to distinguish the good ideas from the bad, embrace the former and reject the latter.

The enemy is not religion per se but religious literalism. The doctrinaire literalist insists on the anthropomorphic deity (or deities) of his choice. The doctrinaire atheist rejects this belief as incompatible with the modern, rationalist understanding of the world. Both are guilty of the same error: mistaking a work of poetry for one of prose. They read:

Tyger, tyger, burning bright
In the forests of the night,
What immortal hand or eye
Could frame thy fearful symmetry?

—William Blake, The Tyger

The literalist takes it as a command to go out in the woods at night and immolate a wildcat. The atheist ridicules it because tigers aren’t created by anyone’s hand or eye. They both miss the deep mysterious truth the poem gestures at.

All of our received religious scriptures are products of cultures far removed from ours. They are filled with atavistic throwbacks to an earlier and other time:

The backward look behind the assurance
Of recorded history, the backward half-look
Over the shoulder, towards the primitive terror.

—T. S. Eliot, The Dry Salvages

The problem with traditional religions is that they insist on clinging to these archaic expressions and applying them out of context to the modern world. The challenge is to separate the gold from the dross: to discard the outdated conceptions of an earlier culture, extract the nuggets of wisdom embedded within them, and pass those on to our children.