Here, Voltaire is clearly criticizing the church as an institution by saying that killing two monkeys is basically the same as killing two priests. Monkeys have always had the reputation of being ridiculous, although they are the most similar animals to humans. Voltaire is demonstrating that priests and members of the church are full of nonsense and absurdity. This was a common belief in the eighteenth century, as the church was challenged by reason.
It is not right to kill anyone and is even worse to kill three people and then two animals. This is all part of the absurdity and irony of Candide. If we were to take the book literally, we would not perceive Voltaire's criticism of society and especially of the religious institution. Another aspect of the church that Candide touches is the possession of land:
"The reverend fathers own the whole lot, and the people own nothing: that's what I call a masterpiece of reason and justice." (pg. 62)
The Church promoted justice and equality, which was completely hypocritical. The institution owned the great majority of the land while many were left homeless. Sure, it did talk about helping the poor, but what was it doing itself? During this period, the church was extremely corrupt and was more worried about increasing it's own fortune than about helping others. Many did not realize this and let themselves be manipulated by the institution. Thankfully, at some time the lands were stripped away from it and were distributed amongst the people. Although, much of the land was given to the already rich nobles, which also goes with Voltaire's belief of life not being just. 