That statement is a fact. And scripture (which has already been posted) also admits to it being done. And no, it doesn't, then, automatically follow that "history is much much fuller [sic] of atrocities that have been committed by satanists, worshippers of false gods and atheists".
Statement was surely not a fact. And you are threading on some dangerous grounds, seems to me, by what can be perceived as defending murderous satanists, worshippers of false gods and atheists. (I'm talking about murderers from those three groups.)
John 16:2 says: "They will put you out of the synagogues. Indeed, the hour is coming when whoever kills you will think he is offering service to God."
Jesus is talking exclusively about His believers who are going to be murdered. And He is primarily referring to non-believing Jews who are going to be orchestrating those murders. As has happened.
Poster here was using his statement that "history is full of atrocities that have been committed by people thinking they are doing God's will" primarily as an argument against Christians, since he is talking to me, a Christian, and he is using God with capital G, he's not saying a god or gods.
Jesus' words in John 16:2 cannot be applied to persecution of anybody except as a persecution of believers in Jesus Christ, and that was not poster's intention, I think. And if it was, he can make a clarification, saying something like: "History is full of atrocities against true Christians that have been committed by self-professed Christians thinking they are doing God's will".
Even that statement can not be directly concluded from John 16:2, but at least there is connection. Because John 16:2 doesn't say that "history will be full of atrocities" of the kind Jesus talks about. He is not talking about the volume at all, but about the nature of persecution that believers in Jesus Christ will suffer. The essence of John 16:2 is completely different that what poster wrote.
Anyway, to move on. If poster wants he can also make a clarification in other direction, like this: "History is full of atrocities that have been committed by people thinking they are doing will of their god or gods."
Until such clarification, to get back to what poster seems to have intended to say: if "history is full of atrocities that have been committed by people thinking they are doing will of Abraham's, Isaac's and Jacob' God" then it's a fact that "history is much much fuller of atrocities that have been committed by satanists, worshippers of false gods and atheists."