I understand the basis for the "never without a condom" sentiment, but I feel this case is not being properly examined. No one asked if he uses a condom when he has vaginal sex with her, yet not doing so can also easily spread HIV. If they're both at a committed-enough level to partake in this activity, then switching to anal isn't going to suddenly spread HIV.
That being said, I don't think there is much bacterial danger. We all have bacteria in our bodies, and unless she's sick with some non-usual flora, it's likely that whatever is living in her intestinal tract is also living in his. I'm thinking that as long as he doesn't have broken skin on his penis, there's virtually no chance of any bacterial infection. The common urge to urinate after ejaculation is beneficial for clearing out the urethra, and likely persisted as an evolutionary advantage for that purpose.
I'm not advocating barebacking in general, but practiced within a monogamous relationship where both partners are free of communicable disease is by definition unable to spread HIV or other std's. The wild card comes with the trust factor -- but I imagine that if they're already trusting enough to go without condoms for vaginal sex, then they're just as safe with anal.