If your wife is HIV+, she should not be using breastmilk for anything. She should not be feeding your baby breastmilk. There is no reason for your wife to be lactating at this point.
I'm not sure why your wife thinks breast milk up the nose would help an infant with the flu. I can't imagine a doctor would think that would do anything. Glad you told her to stop. In general, hiv transmission to newborns takes place IN utero (before born). However, typically an HIV positive woman is not recommended to breast feed. I would say risk is very low if any. Call your baby's doctor to be sure but again, would think any risk is negligible. Is your wife considering Prep?