Big E seems confident that stirring up the old gods is a bad idea. I'm not sure what the Breton is on about with meditating on a mountain. As such, I am loathe to agree or disagree with him.
I could be 100% wrong but I think the argument is actually broader than the old gods.
Motierre is saying that rulers are allowed to, even obligated to, transcend the morality of the common men. That rules that are meant to be followed by commoners can lead to failure in rulers. Basically, realpolitik, ends justify the means, whatever - rulers need to be able to do whatever they need to hold on to their power.
Emperor is arguing that the divine right of kings (meaning that a ruler is justified to have power by a divine authority above them) is necessary because otherwise there is no justification for the power of rulers. As such, rulers should be beholden to rules and responsibilities set by the divines. In our previous conversation together, Emperor seemed to have suggested that he doesn't really believe in the Divines, but simultaneously feels compelled to because the concept of faith kept the Empire together this whole time. So his own belief is very shaky, but simultaneously could be quite strong. In the mind of a troubled believer, typically doubt begets the strengthening of faith and not the weakening of it.
Motierre is bringing up Jurgen Windcaller in order to, I think, make the following point: here is a great man that threw away everything and was reduced by to an idle failure due to a religious calling.
Like you. The conversation already feels like the "Rhaegar was righteous and Rhaegar died" monologue from ASoIaF.
Essentially, to justify his own crimes of trying to summon the daedra, Motierre is trying say that everything should be permissible to men like us while simultaneously tearing down the Emperor's sole support, which is his faith.
I don't think we should let it happen, my dudes.