It may be true that Jim Jones was in fact an atheist. I don't think that matters so much in this discussion. His followers were religious. He used religion and religious practices to snare his victims. He was a megalomaniac. The way he was able to get these people to kill themselves and their children is what is so scary about religion. It can be used against the gullible in horrific ways.
Could an atheist use religion to do bad things? Yes. I think it happens all the time. I would bet that most religious leaders don't really believe what they preach. However they have figured out how to get what they want by using the brainwashing techneques of religion and the power of using superstition and delusion to convince people to follow them.
So could this happen to a Humanist group? No. You have to have followers that are able to be manipulated by religious belief. Humanist and atheist would not fall for such things. We are skeptical and demand proof. We are free thinkers and would not be suceptible to the kind of mass delusion that religious people are.
So yes Jim Jones could have been an atheist. His followers however believed he was the son of God and that they were going on to their reward. They believed he could heal them with powers given to him by God.
There are bad atheist and bad theist. There are good atheist and good theist. Sometimes bad atheist can use their knowledge of just how gullible humans can be when it comes to the supernatural and superstitious beliefs against them.