The singer spells it Raffi.
I think it's not that uncommon as a childhood nick for
Raphael, esp. in other parts of the world where
Raphael might be more common. It seems extremely unlikely that people would think that was a negative connection. The nickname of the 4 year old
Raphael "Raffy" I know might make people say to themselves,
Oh, now I get it, Raffi the singer is short for Raphael! but it certainly isn't worth mentioning as a connection since they call him
Raphael much of the time and it's obviously a short form of
Raphael. I'd think that when
Raphael is old enough to get annoyed by people singing Raffi songs at him, his would-be teasers would be way too cool to sing Raffi songs out loud anyway.
Anyway, I'd call my son Raffy if his name was
Raphael. YMMV