Ahhhhhh this has basically been my assumption, too, SO AWESOME. I am 99% sure that Thomas was actually kind of a jerk, but Athos was (and continues to be, to a certain extent) completely blind to the fact, in the way that he can often be blind to the faults of the people he loves.

(There are a couple things in S2 that support that chain of events, in my mind, or at least don't contradict it. And that's all I will say. :D )