I think there are some valid critiques that apply to both sides.
Silver does have his biases and definitely likes Goff. He was the same way with Kurt back in the day, and if I remember right, he wrote the first major article in SI when Warner exploded onto the scene. He doesn't really try to hide his bias, but that doesn't negate its existence. On the flip side, he doesn't report bullshit or make things up out of whole cloth, at least in my observation.
Aikman is a smart analyst and definitely knows football, no question about that. But he is hypercritical sometimes. In this instance, it appears what Silver wrote touched a raw nerve, and not only did he respond in a very defensive manner, he did not say anything to refute the reporting about what happened in the production meetings. If there was nothing to it, he could have easily said "the critiques of players are mine and mine alone and never originated from discussions at the production meetings."