This is a first of hearing this. Have you tried to restore her iPhone and set it up so you both have separate iTunes accounts?
You'll need to have iTunes recognize both of your iPhones as separate ones and transfer the purchases of her apps to her iTunes; same with music, although music is harder unless the music was purchased through iTunes.
Here is a support link for making separate iTunes accounts.
The phone number in the messages settings is tied to the SIM card or the phone itself, so unless his SIM card is in her phone it's more likely that the culprit is his email account being in her messages settings.