Tommen is looking toward the window because outside the window is where the sept, the trial, and his wife are. I don't agree that Tommen is thinking of jumping out before the sept has even blown up.

It would be improper for anyone to sit down in the presence of the king, therefore the High Sparrow asks permission. By doing so, he acknowledges the authority of the king and diffuses the tense situation. This is responsible and consistent characterization, not clumsy filmmaking.