If you look back in history you will find that there were many human cruelties prior to the invention of the modern secular human.
You might want to look at the crusades, for example. They killed a few hundred thousand people. The inquisition were also fairly inhumane. Ignore the mortality count and you get another whole list of non-fatal misery caused by religion - female circumcision, hatred of homosexuals, prohibition of interfaith marriages, etc. These all predated the widespread secularisation of the 20th century (although I think you're exaggerating the extent of that secularisation).
Now it is clear that a few hundred thousand people (Crusades death count) is small talk compared to the achievements of war in the 20th century. But this is mainly due to the fact thats that
a) pre-modern religious conflict occurred in a very different demographic framework to 20th century war. In the middle ages, it would be impossible to kill millions of people for example. A few hundred thousand is actually a remarkable effort in a land occupied mainly by rural people.
b) the superior death count of 20th century war is clearly due to technological advances. In the crusades they had battering rams, swords, bows and arrows, etc. The 20th century was inventive enough to come up with industrialised slaughter houses and nuclear bombs.
given these differences, comparison of "body counts" becomes a bit silly.
mick