Well, if you are a deity, it is in you best interest to have the greatest number of followers; even if you don't directly get power from faith and worship, you still get minions and agents...

So, if you are an evil deity, it is smart to promote a non-evil branch of your church that is dedicated to the most palatable aspects of your dogma. Like, Malarites would be interested in attracting non-evil hunters to their flock, Wee Jaas's church would be interested in attracting mages and morticians, the church of Hextor would be interested in attracting warriors and authoritarian rulers,... etc.