Stealing is wrong?
Stealing is immoral, as it is causing harm to another by depriving them of what is rightfully theirs. This is not indoctrination.
Lying is wrong?
Lying is wrong only when done for purposes that lead to harm to another. It can also prevent such harm, such as telling the Nazis that there are no Jews in your attic. Teaching a child that lying is ALWAYS wrong is indoctrination.
Rape is wrong?
Rape is immoral, as it violates the victim's free will. This is not indoctrination.
Murder is wrong?
Murder is immoral, as it violates the victim's free will and causes pain in the lives of their loved ones. This is not indoctrination.
Disbelieving in God is wrong?
There is nothing inherently moral or immoral about believing in a god. It would be indoctrination to teach that either is wrong.
Morality comes from empathy. Things are wrong because they harm others, we know they are wrong because we wouldn't want them to be done to us. The Golden Rule, is basically empathy put into words. Jesus was not the first to do this, he most likely got it from Rabi Hillel who was an old man during the time of Jesus. "That which is hateful to you, do not do to your fellow. That is the whole Torah; the rest is the explanation; go and learn." However, this idea has also existed in many other cultures long before Rabi Hillel ever spoke these words. Confucius, who died in 479 BC said, among other things, "Never impose on others what you would not choose for yourself."
You can say that it's only my opinion that harming others is wrong, but that would be incorrect. It's a long established tradition, that spans nearly every culture. It benefits the culture as a whole, as it creates an environment where you and your loved ones can be safer. The legal system is a reflection of this, as it's primary purpose is to deter those who would harm others via punishment, thereby making our society a better place to live.
You can still say, well that's just society's opinion. But this would be as wrong as saying that believing that I have hazel eyes is opinion. It's an observable fact that I have hazel eyes, and it's also an observable fact that refraining from harming others creates a society where everyone benefits.
"If it's wrong to hurt someone, and you are someone yourself, it would be wrong to disbelieve in God because studies show doing so, decreases length of life."
I found the study that I believe you are referring to and it has nothing to do with a belief in a god but only attendance of church services. Atheists were not a part of the study. The study was about churchgoers and non-churchgoers, both of theistic beliefs. The shorter life-span of those theists who do not attend church could be due to stress caused by the guilt of not going to church. Atheists would not be affected by this stress as they would not have that guilt. However, I admit this is speculation on my part, but it's very reasonable to assume this.
And besides, what I do to myself, while it may be unwise, has nothing to do with morals. Morality has to do with causing harm to another person. Take rape and S&M for instance. Rape is always wrong as it violates the will of the victim weather it causes physical harm or not. S&M, on the other hand can cause pain, subservience, humiliation, etc. but it is always consensual. No ones will is being violated, hence there is nothing immoral about it.