One of the main ideas in Yakumi Sarai's works is that Gensokyo is the last resting place of things that are no longer believed in. In this case, human sacrifice was abolished in the outside world and so it now has to exist in Gensokyo because it is the very nature of Gensokyo is to carry on with the customs that no longer practiced outside. Failing to follow the custom would defeat the country's whole purpose and presumably do irreparable damage to the magic that maintains it. Yakumi Sarai plays this sort of tragic situation very well in my opinion.
I think THIS is the message to take from this doujin. Gods are only maintained through faith, and the humans of Gensokyo worship their gods through human sacrifice. If you reread page 18 and 19, Kanako and Suwako themselves didn't like the idea of eating a human being, either.
Upon knowing that Kanako and Suwako would accept, Sanae immediately labeled them as "evil", similarly to how she labeled humans the same way in Yakumi Sarai's other doujin, "DODO". She grew a little then, and in having faith in Kanako and Suwako (who explicitly said they want her to stay around forever), and accepting the offering, she receives faith, and becomes a goddess herself.
Humans can't be placed under the tentpole labeling of "good" and "evil", and neither can deities. Both life forms must have to do what they can to stay alive, even if they don't like it.
I honestly didn't catch all this until someone on Danbooru spelled it out for me. While I don't agree with the message, I feel like I can accept the story. I wonder how Yakumi Sarai will portray Sanae after this, though?
This concept makes me wonder how aztec deities would fit on Gensokyo, shame that only Japanese in origin gets into.
