Just because you don't see it, doesn't mean it isn't there
To use a popular reason
I've never found WWTW? vindictive of religion or atheism either way. It merely states that in that particular case, where the Mintakens turn religious because of Starfleet's interference, shouldn't be allowed to continue. Not even because it's religion, but because of what caused the religion to develop.
Also, one messed up scientist does not "many of the greatest atrocities on our planet" make. Frankly, the more I think about it, the more ridiculous this statement because. Sure there have been some horrible events, but very, VERY few of them in the name of pure