Realistically, a good and experienced captain like James Kirk WOULD have raised shields in that scenario in the movie.
We can't apply our own standards of "realism" here when we clearly see Starfleet has different standards. Kirk didn't raise shields when meeting fellow yet mysteriously silent starships in "Omega Glory" or "Tholian Web", nor did Picard when meeting with the fake Yamato or the Lantree. Hell, there isn't even indication that Picard would have raised shields against Ben Maxwell's rogue Phoenix initially!
There simply is no precedent for raising shields against a fellow Starfleet vessel.
Timo Saloniemi