Phrased more charitably, "protecting his turf" is actually "doing his job."

With the little information available, I can see the captain's position. The programmer was new and rolled out changes to the surprise of the captain. Programmer hadn't earned captain's trust yet, and was pushing out new procedures which the captain did not (?) agree with. That'd be a no-no in any company, just substitute CEO for captain.

Regardless of whether his system was fantastic, the manager in any org is meant to be a safeguard, even when it feels like a bottleneck.