Although within the story of his-story there have been atrocities in the name of religion, the greatest horrors have not come from religion, but from power/politics, greed/economics and science devoid of 'heart.'
The crusades and the inquisition pale next First World War trench warfare or Nagasaki and Hiroshima. The 20 th century is the bloodiest so far in history and the science of weaponry has more to do with this, than any religious belief. Even so called religious wars -when looked into- were probably more about power and greed than about religion. Religion was often just 'hijacked' to 'legitimize' it for those who needed an excuse...but if it had not been available, it's easy to imagine that other justifications would have been found.
Science has given us the medicine against polio? Wonderful! It has 'given' us medicine as well as its many side effects. It has given us electric light as well as weapons of mass destruction. It has given us mechanical flight as well as pollution.
Religion has given us -next to 'the bad' you're so concerned with- some 'good' also. Pyramids, temples and cathedrals were the first attempts at great engineering and architecture. There is the requiem of Bach and the ave maria. Art of da Vinci and Michel Angelo, the Bagavad Gita and the Upanishads, Rumi and Hafiz, and the compassionate hearts of the Dalai Lama and mother Theresa.
Logic and intuition both have their place in this play and are inseparable. Only in dualistic imagination is there a 'clash' between the mountain and the valley.