Firstly, that's old lore and not necessarily true anymore.
Secondly, Boethia isn't necessarily bad. He/She wants mortals to be strong and independent ]
I think there are two points of note in this.
First, Boethia, while manipulative, fickle and generaly unpleasent likes to test mortals to become the best they can. Theres nothing wrong with helping others so long as you don't let it compromise your strengths. Boethia can also encourage mercy, as someone you save one day can be someone to be used another.
Second, if you think about the Vigilents of Stendar, they are a religious order. more specificly, they are a religious order which, unlike Daedric Cults, does not have actual contact with their god. Stendar and Boethia could still be tenious allies on the higher/lower planes, but the church has no way of knowing, because Stendar doesn't directly communicate with them. What the Church says, and what is actually going on, are probably quite different.