Revolutionary atheists vs Stockholm syndrome (John Gray)

Esteemed cosmologist, and my old friend, Andrew Jaffe just posted a quick retort on his blog to a long essay by philosopher John Gray. Gray has an objection to the strident challenging tone of modern atheist thought-leaders like Sam Harris and Richard Dawkins.
I am not the scientist Andrew Jaffe is, and I was hopeful that Gray’s essay was something endearing and woolly, a plea for magic in our contemplative moments. Some time ago I began having issues with my atheism, a matter of personal feeling about this great universe. I’m not sure even now if I am proud or sheepish about it, but it is what it is – I am a woolly atheist.
Gray’s objections alas are very different, and worrisome. Supposedly Gray is discussing why militant religion is in resurgence, but Gray – himself a self-professed atheist – really writes to vilify and blame, cheekily calling the New Atheists “missionary” and “evangelical,” and less cheekily comparing them to the pseudo-scientists who justified Nazi and Soviet genocides.
It took a while for me to understand: John Gray has Stockholm syndrome. He’s been living in a culture that has been deferential to the religious for a very long time, and he can’t see a way past that.
Modern atheists are revolutionaries, not missionaries, and this is their revolution: to insist that in the modern world — where we fly without feathered wings, talk across distances without magic crystals, kill far-away enemies without thunderbolts and stop epidemics without human sacrifices — religion must now justify the exalted place it demands in the making of public policy and education. 
Of course it’s messy and truculent. Suffragettes and Freedom Riders and Stonewall gays were messy and truculent too. Of course red meat gets thrown, to fortify the beleaguered and discouraged. This is how it works, always. For Gray to insist that change come in nicely and politely is a ludicrous misreading of history.
Gays don’t want to destroy straights; feminists didn’t want to replace men; American blacks had no intention of visiting the appalling crimes they endured on the children of their American white tormentors. They wanted an equal playing field, the chance to participate as freely and with as much respect in the many forms of public life as their counterparts did.
Atheists don’t want to destroy churches (and most of us will even give their tax status a pass, for now). We simply want to make sure churches don’t get an extra say on matters of serious public policy, just because they are churches.
Just because you believe God won’t let humanity drown itself in carbon, you don’t get to deny it is happening, without data. Just because you and your holy book don’t like same-sex love, you can’t selectively deny others the same right to cohabitation and tax benefits, or push glorified torture like conversion therapy into the sphere of real psychology. Just because evolution makes you profoundly uncomfortable doesn’t give you a right to shove your ancient myths (which don’t even mention dinosaurs, much less DNA) into a science class. Just because you don’t like a medical procedure’s greater social implications, you don’t get to deny it selectively in the health care you provide under government rules (whatever the Supreme Court says; they were wrong about ‘separate but equal’ too, for a while).
Speaking as an atheist (albeit a woolly one), I understand religion has had an ancient and often noble place in public and private life, and that we may even be wired to perceive the world in its way. If a public event opens with a prayer, you know, whatever. When I stare up at the night sky I too am filled with wonder, and even I can be touched by the community of worshippers.
But the religious don’t get a free pass to challenge science and public policy with nothing more than feelings. This is the revolution. Sorry it’s not polite, Mr Gray, but you might want to reconsider the beam in your eye before faulting the mote in another’s. A philosopher should examine himself with more rigor.