I am honestly baffled that you cannot see why the player in question is becoming so frustrated. In the first example you gave where he complained, you made a critical mistake, which is essentially telling him that he has no say in how his character should react to given situations.
Why can't characters in your world estimate the given power of a character that can, if he so chooses, stop the flow of time, summon Angels from the heights of the Heavens, cause the earth itself to shift and break apart in a massive radius, etc.
And if the players character has any inkling that the person he's attempting to stop has this level of power, it's perfectly reasonable and in fact logical to retreat rather than pointlessly throw his life away. But no, according to your DMing style, the player should just shut up, play the encounter out, and do what you think his character would do, since you know so much more about roleplaying and how his character would react in the situation.
Do you really not see how that can be frustrating to a player? All I'll ask is, if the players had decided to retreat, what would have happened? Because it sounds to me like this was a railroad encounter they couldn't avoid and the player you're talking about annoyed you because he objected to this.