When I refer to God, I speak of the Judeo-Christian diety, not the moon god of Mecca. Yet even Islam produced more moral behavior than the brutal despots it displaced. There was a time in History where Islam was actually a force for relative justice. As soon as it tried conclusions with Christianity, it was turned back. The better yields to the best.
As for your last point, the 'atrocities of the middle ages', while horrific, are lesser in magnitude and multitude than those of our modern 'enlightened' times. They are also less when compared to the barbarism of the times. However bad times were, they would have been worse if Christianity had not taken root. No force on Earth, relative to the strength it possessed, has been so restrained and beneficial to mankind as Christiandom.
Playing the body-count game does not change the argument. People are what they are, and adopt the theology or ideology that justifies what they want to do anyway. Or, in the case of truely evil people, they twist or pervert ideas to fit their ends.