Why "even atheists"? Historically, atheists are not even close to the biggest aggressors against Christians. That would be other Christians, probably followed by Muslims (during the ascendancy of the Caliphates).
On the other hand, clearly many atheists allow others to have different beliefs, including Christian beliefs, and to allow religious texts to be distributed (such as the Bible).
This seems to be much more about power and control over the Chinese people.
In particular, you have Catholic France against the Catholic Habsburgs, and the issues were not doctrinal. Not what you would expect if this was a war about religion. This was not a war about religion primarily, by the time most of the deaths occurred.
But to your specific point, France only entered the war almost twenty years after it started.