Maybe he was recovering from a sickness? If you miss the train, you have to get some alternative transport - there isn't another one. His Dad would probably be able to Apparate with him to Hogsmeade, or they could use Floo Powder, a Portkey, or a broom. Whatever you decide, it can't be directly into the Hogwarts Grounds, it'd have to be in Hogsmeade. I think it's like an hour away walking, less time in a carriage which would probably be arranged by the school for him.
He'd probably be sorted in the Headmistress' office, where the Sorting Hat stays. :)