You'll really want to hear from e.e.norcod on this (you might try sending him a PM if he doesn't post in response), but my belief is that, as long as there are no cuts or open wounds that the alcohol can use as a pathway to the bloodstream, you should be in good shape. Rubbing alcohol IS a poison, but not a contact poison. It can be absorbed through the lining of the colon (large intestine, rectum), so it should only be used on the exterior surface of the rectum. By the same token, she should avoid licking the treated areas until after it has an opportunity to evaporate.

It's also a drying agent, so swabbing inside her vagina prior to intercourse could cause tearing of her lining, which would result in increased risk of exposure to sexually transmitted diseases and possibly yeast infections (and bleeding, of course).

All in all, I'd say it was a pretty safe practice, and a clever idea.

(Now waiting for the expert to weigh in....)