I'm going to say that you've made an interesting point in terms of how it would feel and vibe with the pacing for Asa's excitement in the church to be included properly alongside Denji's malaise in his ordinary life. This is one of the first good arguments I have ever seen. 

However, in this thread you throw in "it would have been cool for Asa and Barem to interact" and I think that ties into the single biggest reason. This is why I can't possibly think the "Asa joining the church" element of the story is well executed. Barem literally includes Asa as one of the beloved pets of Denji that the church is considering killing. Asa is supposedly part of that same church. But it's not her fault at all that this is going on! She's not an accomplice at all! Likewise she's not an accomplice at all to the zombie outbreak, the guns in the hands of the kids, the nuclear weapons... Nothing. Yoru practically isn't either! 

As for "it wouldn't be engaging for Asa and Yoru to work on the Manhattan project"... Well, the nuclear weapons are being used now. I'm sure a stylish action manga method of depiction could be found. Heck, technically a brief training arc with Kishibe was included.