It was very much in the spirit of nothing is true and everything is permitted. Nothing is true for what we once may have thought about Assassins being the heroes and Templars being the villains. A pattern consistent also to the AC comics that tied into the games particularly the arcs of Nikolai Orelov, Innokenti Orelov, and 'Daniel Cross'. Honestly I felt that reading specific comics adds more complexity to the story.
Their alliance was sadly short lived and more so having had trouble getting along with my own father I emphasized with 'Connor' regarding Haytham as well as Desmond regarding William.