... I think MC could actually stop that rain. Why didn't he do just that?
Because it takes a while for him to prepare for the big spells/miracles (or whatever it's called). For the simple stuff, he only needs a few spirits. But for the really big stuff, he probably has to go around gathering spirits and have them coordinate their combined powers. Also, it was mentioned that the spirits will do stuff for him, because High Elves are essentially their equals. If he goes around abusing his powers and getting hundreds of spirits to fire off big spells all day, everyday, then there's probably some sort of repercussion afterwards. I'm guessing something like the spirits would ignore him, they run out of power and it takes time to recharge, or it rains somewhere else instead and causes a flood that wipes out a village.