Is it true that atheism has killed more people then organized religion?...

[Existentialist]

The problem is that it promotes violence and says the god or the church said to do it, one example is
islamic governments putting death penalty because their religion says so

Completely disagree. All governments, including islamic ones, are coalitions representing different interests. In Iran or Saudi Arabia, the government is answerable to a complicated alliance of ruling interests, many of them commercial and definitely not primarily interested in religious observance, though they may use religion as an excuse to intimidate their opponents and weaker class interests. The point is, getting rid of religion won't get rid of the underlying class antagonisms. Being atheists doesn't absolve us of the need to understand the economic forces at work or the political reasons for the existence of oppressive governments.