Especially for LDS and Friends!

I would comment on both areas separately.

Review the novel as is. Give critical feedback on style, plot, etc. Be as thorough as possible, while encouraging at the same time so he doesn't grow bitter about any of your comments and decided to ignore you on the doctrine aspect.

Then include notes on the spiritual aspect. I'd send the comments privately, but include the comments in your notes so that if the topic does come up during the discussion you have them on hand. I'd also try to find some articles and quotes from true LDS sources to back you up just in case. I'd be sure to point out that it's fine if classified as "spiritual/religious fiction", but as is does not fall under "LDS fiction" and will most likely not be picked up by any LDS publishers/retailers as is.