I was going to answer and then I saw Lady Nerevar is reading the topic lol.
And then Lady Nerevar left without posting anything
Gods in TES aren't omnipotent beings. They're closer to the gods of the Greek/Roman pantheons in that they have human failings. In this case, Boethiah wasn't happy with Trinimac interfering with the Chimer, and decided to teach him and his followers a lesson.