@narutaki
If I recall correctly, it was implied early on in the manga that he behaves that due to the goddess' divine protection. A form of geas to "enact justice", or some shit.
@Le_Butters
While "kill them all" is indeed a bit much, readers will come to that conclusion when the story keeps egging them on. With a powerful MC, whom especially desires to "destroy all evil" very aggressively, it may as well end up being extremely irking when the MC...Does not act on any of his emotions, or his presented superpowers that can completely ignore the world's order.
So while what you say makes sense, it's also equally hard to justify it when your MC has every convenient tool and "protection" to just do whatever flying fart he wants.