The skipper is responsible for the safety of all persons aboard, adult and child, in all conditions. Newbie sailors, in my experience, tend to be either overly cautious or -- worse -- overly confident. As they gain experience, and the sea whacks them a few times, they begin to achieve a more desirable condition of being knowledgeable, experienced, and.....cautious.
In my opinion, with a 39' light displacement boat it would have been prudent to reef before the wind reached 25 knots, especially if you were beating to windward in a narrow channel.
Remember, however, that there are several ways to reef safely and that ANY reduction in sail area can be very helpful in relieving strain on the boat and the crew. For example, you can just roll up the headsail....all the way. That leaves you with only the main to deal with. Under main alone, most boats will tack to windward OK, but will do so VERY slowly. Losing the headsail has the effect of a brake...you slow WAY down. And, usually, the boat's motion becomes more liveable and you can better work on deck while you reef the main. Or, just drop it entirely if conditions suggest. Then, roll out as much genoa as you need. Most boats will tack very well to windward under genoa alone.
No one can tell you how best to deal with the skipper when you don't agree with his/her decisions. But equipping yourself with some knowledge of sailing, and participating in, e.g., sail raising, reefing, steering, navigation, etc.....can earn you big points when it comes to challenging the skipper.