Thank you Atoli! *edited*
Okay before the raping/whoring is blown up any further, let me clarify I only said "I wouldn't put it past him" - I'm not saying Aymeric was conceived against the will of the mother, or even that it is likely, but that Thordan doesn't care if other people suffer from his actions (as Rosenoire pointed out, not even for his son) or is in another self-serving delusion about them.
This might have been different at another time, and yes, there is a certain similarity in the eyes of father and son that indicates Thordan must've been handsome in his younger days, and probably very charismatic if he made it to the position of Archbishop. There sure were a few women that fancied him, and to imagine a lowly noblewoman thought she'd get something better out of an affair with the Archbishop than out of an arranged marriage is not that hard.
So the range of circumstances under which Aymeric could have been conceived is rather large and doesn't give us any better clue about who his mother was or how he was brought up.
On Thordan's motives, I'm sure he is a complex character and his choices were no easy ones, but the choices he made in the end, playing safe and having the majority of his people suffer, as well as having his own son tortured, tells us he was corrupted by his power and had little feelings for Aymeric.
Their tries to persuade the other of their views were not born out or respect or trust, but necessity and a false hope in their blood relation. Aymeric saw what a good father looked like when he spent more time with the Fortemps, hoping his father would think as much of him as Edmont thought of Haurchefant. Thordan thought his flesh and blood would think like him, and was completely deaf to his arguments. If there had been any value for his son, he would have listened and given his son's views a thought, but he simply dismissed them. In their actions, they showed how little they knew each other.
In the end, Aymeric had little problem having his father killed, just as Thordan had had no problem having his son tortured.