We have a walk in attic. A new roof was just put on and the old roof (3 layers) was ripped off, new plywood put down, roofing paper and then shingles. The problem is that the roofing nails came through and protrude as much as 3-4 inches into the ceiling of the attic which slopes down from a ridge. They are very dangerous.

Is this the normal way to install a new roof? If so how can the danger be averted? The roofer suggested insulation and wall board over the rafters to hide and prevent exposure to the nails. Is this the best solution?

Roofing nails are not 3 or 4 inches long to start with and would never come out that far into attic.

Roofing nails do come though, into attic, that is normal

Agreed, roofing nails do come through the roof. But the nails should not protrude below the rafters. If you want to use the space, put up sheetrock on the rafters.

A lot depends on the climate where you live.
Don't insulate and wall in an attic until you research how to do it properly, with the proper ventilation. You can have a rotten roof, popping nails, dripping condensation, and brittle wiring in 5 years if you don't.
Ridge or gable or hipped side above ceiling vents.
Venting channels between rafters.
No blocking of soffits.

The roofer used a framing gun instead of a roofing gun when installing the shingles. This is not a problem as far as holding goes.

As joypulv said check on ways to correctly finish and insulate.

Chuck