People will always find a way to justify their actions, be it religion, race, political ideology. The fact is that people do good things because of their religion as well as bad. In fact invariably you will find that the bad actions are often contrary to the spirit of the religion - the Chant of Light says that all people are equal in the Maker's eyes, to harm to someone without cause is wrong, to steal is wrong and to lie is wrong, not matter who that person is. Unfortunately, very few people in positions of power seem to think they have to follow this code, hence the inequality in Thedas society and the reason that some of those who are oppressed by the system think they will be better off under the Qun. However, this is probably because they don't know the full extent of the religion they are adopting. Sten and Fenris give a much more accurate insight into this than Tallis because they are not trying to sway you by their arguments, just stating facts. Sten was genuinely puzzled by the society he encountered with the Warden because he had been brought up from birth under the Qunari code. By contrast my Wardens were equally puzzled/appalled by some of his statements but so long as he offered no threat to them or their mission, were prepared just to let it go. I tend to play elves, so my first three wardens were Dalish elf, female elf mage and City elf. None of them liked the sound of the Qunari even though they were largely hostile towards the Chantry. This was largely because you could operate in general Thedas society without being a devout Andrastrian - mostly as I point out above because society is not run according to the Chant of Light. Whereas to adopt the Qunari faith is to adopt a total lifestyle and this is required by those in charge in Quanri lands - naturally those still living outside of those lands are not bound by the full extent of those beliefs because there is no one to enforce them. Sometimes they also allow a degree of leniency whilst new converts are adapting - as in Rivain where they tolerated the Wise women seers until such time as they had been able to educate the young to reject them.
It is interesting to note that Tallis' scroll contains the names not just of current members of the Qun but according to Tallis those who have left it. Since she cannot possibly know the names of every Qun convert, is it not conceivably possible that many of the names on the scroll were in fact not current Qunari but ex Qunari? In that case, that would most likely make Salit a double agent, the Ben Hasrath wanted to list to fall into enemy hands because they were banking on the Orlesians engaging in mass slaughter, which would aid the Qunari cause by causing greater resentment in the Alienages and have the bonus of eliminating defectors. Not enough is known about Salit and his motivations to be able to say anything for certain but if he was a genuine Tal Vashoth or not, it was the list that that Tallis' superiors were not bothered about recovering, not simply Salit himself. Clearly they were not as bothered about the implications for possible "innocents" as Tallis was.