Discworld and religion is an interesting subject to discuss because Pratchett is a good writer, so it is possible to discuss it, but I don't think he's pro-religion. The article kind of implies that the 'proper' cosmic authority in Discworld are the good guys, while notably leaving out what is very obviously the most developed and recurring cosmic authority in the setting, the Auditors of Reality. They are definitely not good guys and they hate human beings, and particularly human imagination.
The Auditors of Reality could never be the good guys in Pratchett because it's impossible to imagine Pratchett unironically legitimising any authority which has their amount of power relative to everyone else.
It's been a very, very long time since I read Small Gods so I'd have to re-read it to do a specific analysis on it. But I agree with the article that it's a wider book than just being a narrow critique of religion.