I think she has definitely been touched by someone. The problem with this age is girls re-direct the identity of the offender often. I'm not exactly sure why this is, but when molested will often point to a "safer" perpetrator - i.e., one who can't hurt them anymore or was unlikely to hurt them in the first place.
In a case like this where a man living there would have opportunity at a variety of times to have done this, it is fairly believable.
A doctor's appointment is very very unlikely to be able to turn anything up unless he's given her an STD which seems unlikely.
At the very least, the answer is absolutely no, he can't come live there again. And I'd tell him why.