That's the biggest problem when the story. It assumes you know a lot, especially from the books. Elites are supposed to be friendly, yet they are just a "fanatical group" with no real explanation. A lot of details are just glossed over.
Really anything to make it clear that these Covenant aren't The Covenant would have helped a lot. The closest they ever come is in the description of SpOps episode 4, which refers to "cult leader Jul 'Mdama". But this tiny bit of information is too little, too late, in the wrong place.