The Ori were once part of a race of humans called the Alterans. The Alterans lived in a distant galaxy and were very advanced; the most advanced race to have ever existed. A philosophical divide grew within the Alterans: one whom we now call the Ancients and one whom we now call the Ori. These two groups became more and more opposed. The Ancients pursued science and rational thought while the Ori became more and more fervent in their religion. At one point, they broke altogether and became enemies.
The Ancients, being committed to freethought, were absolutely opposed to violating anyone's free will. This was not the case with the Ori, who were fierce in their religious convictions and not above killing the Ancients. They began to amass an army against the Ancients. The Ancients were philosophically and morally opposed to killing or even interefering with others' choices. As such, they chose to conceal their level of scientific progress so as not to exacerbate the situation with the Ori.
One of the Ancients devised a weapon, The Ark of Truth, which makes anyone who looks into it brainwashed. The purpose of devising it was to counter the lies the Ori spread to get people to submit to their religion. Use of this weapon, though, would violate their followers' free will and, as such, they agreed not to use it. Instead, they built an advanced spaceship and set sail.
The Ancients and Ori both eventually ascend. The philosophical differences they had as humans continue even into their ascension. The Ancients, being dedicated to scientific thought and philosophical principles, have a strict non-interventionist policy with the lower realm. They feel they have no right to play God with the lower realms. As the pacifists they are, they will not even intervene in self-defense; preservation of free will is the highest moral law for them.
The Ori do not share this. Their religious convictions have led them to a sense of entitlement as it were over the lower realms. They feel as higher beings they have a greater truth than those on the lower realm. As such, they command all humans to submit to their religion, Origin. By believing in the Ori, the Ori harness the power of their followers.
The Ori cannot stand the Ancients who are dedicated to science and do not submit to their religious convictions. As such, the Ori are still bent on destroying the Ancients. Once they learn of the humans in the Milky Way Galaxy -- the Ancients having been shielding our existence from the Ori -- they begin to amass an army of followers to conquer the Milky Way by spreading Origin.
Even though the Ancients know that the Ori's ultimate purpose is to destroy them by harnessing the power of the believers in the Milky Way, the Ancients refuse to intervene. Even though Origin is a lie, they refuse to violate the free will of those who wish to follow.
The religious criticism in the last two seasons of Stargate SG-1 does not go unappreciated. The ultimate moral of the arc is that of rational thought versus dogma. There is a strong emphasis on not forcing someone else to believe and promoting critical thinking over blind submission.
There is a second aspect which is explored in all this: killing people for what they believe. The Ancients represent one extreme of the spectrum in that they will never kill anyone for what they believe nor influence what anyone else believes, not even when that belief is damaging to the individual or will inform aggressive actions against others.
The humans from Earth represent somewhat of what Sam Harris advocates. They attempt to always reason logically with Origin followers about what they believe. They won't forcibly prevent someone from believing in Origin. There comes a point, though, where they recognize it may be ethical to kill someone for what they believe -- the sentiment from The End of Faith which is so frequently quoted out of context. Origin teaches that the unbelievers are wicked and must be given the opportunity to convert. If they refuse, it is your duty to put the infidel to death.
With Origin holders having this belief, it is a fine line the humans from Earth consider: when is it ethical to kill someone merely for what he believes?