At first I thought, "Clever". Then I wondered, why bother? He had to take time out of boat management to coax an obviously useless crew out of the safety and out-of-the-wayness of the v-berth. The EPIRB was set off either way. And then he had to call off the rescue, which probably did not win over the heart of the panicked crew.
I suppose it's possible that in the intervening time (between setting off the EPIRB and the flyover) he could have convinced the crew that they didn't need or want rescue, but that wasn't mentioned.
So looks like the options are:
1) Do what the skipper did, and convince the crew after the fact to cancel the rescue. Ideal, since everybody is on board and no backs had to get stabbed.
2) Say to the crew, "Look, I know we don't need rescue. If you set that thing off, I will just cancel the rescue when arrives." And if the seem to be listening to reason, "It would be irresponsible to do otherwise, since a rescue would be dangerous for us, dangerous for the rescuers, costly for me, and costly for the rescuers, and a waste of resources that might be more needed elsewhere." The crew will resent my decision but at least there will be no surprises.
What did they end up doing to handle the storm?
1972 Catalina 27