Yes, religious concerns absolutely played a role (both regarding Sunday scheduling and issues with culture), but there are other factors as well, ranging from research output (important to P12 and B10 among P5 conferences) and recent on-field performance (leading up to Pac10 expansion Utah had all the hype as multiple-time BCS busters). We all know religious issues played a role, but those aren't changing so we do a disservice when we don't look at the other factors that could change in order to make ourselves as attractive as possible.
The one thing I have to disagree with from your post is that a bonus reason for BYU not being in the PAC12 is that independence makes BYU a lot of money. Yes, independence makes BYU more money than they got in the old MWC, but it's nowhere near what they'd get being in the PAC12. Right now, it looks like BYU gets about the same TV money and exposure as being in the AAC (or possibly a bit less), nowhere near what the PAC12 would get them. If the only thing keeping BYU out of the PAC12 was the amount of money BYU makes as an Independent...well, then there wouldn't be anything keeping BYU out of the PAC12.