7. The Clerics
Back when the identity of River Song was just a glint in Moffats (and Rorys ) eye, her appearances were an addition to an already exciting plot, rather than the plot itself (although I have no problem with either). Funnily enough, in her first team up with Matt Smith (in The Time Of Angels) she isn't the biggest mystery. What really confuses are the militarised clerics. Here the clerics regarded the Doctor with real respect, looking up to him and even warning him of Rivers destructive role in his future. When we see them again in A Good Man Goes To War, about a century or so later in their timeline, they still regard him as a higher being, but this time theyre creating a weapon to destroy him. Why they call themselves the Church is dismissed away by the Doctor in their first appearance (theyre an evolution of the modern religions here on Earth), but we never get a hint at what causes them to take a complete u-turn against the Doctor. It cant have been the Silence controlling them as theyd been rendered weak by the moon landing footage and given they knew River would be trained to kill him, it paints them as a pretty dumb sect.
Potential Solution: They became more financially than religiously motivated and the Silence bought them out.