Never a doubt as to Tom's loyalty. In addition to loyalty being ingrained in his character, he also (as we saw) needed the family and desperately wanted to be a brother--even more so than consigliere. I think Michael was telling the truth when he told Tom (after the Tahoe shooting), "Right now you're the only one I can completely trust."
Ntra la porta tua lu sangu � sparsu, E nun me mporta si ce muoru accisu... E s'iddu muoru e vaju mparadisu Si nun ce truovo a ttia, mancu ce trasu.