@Uooper, with a vast historic of earthquakes, tsunamis and other natural disasters plus the heavy cultural influence of Buddhism, I really doubt any individual or society would love to be under an almighty supernatural entity's whim. No one would love to have a multimillionaire screw over with their lives just for unjustified amusement as well.
The concepts sold and ingrained in manga that you find so annoying are "bringing down what is supposedly untouchable" and "every religious sect or big organization unquestioningly holds political power" and both are plot devices that have every right to be used considering humanity tragedies induced/caused by religion (as some sort of reminder to avoid it or not repeat it again, if you exaggerate the interpretation).
So... Welp, you are searching for entertainment material in the wrong place. Just accept it and move on (or not, I'm not your mother).