All selective colleges want and expect to see an upward trajectory of grades. When senior year grades slump, colleges begin to wonder about a student’s drive and commitment to their academics – and that can effect acceptance at any college. Although I understand your concern about Yale’s deferment, I would impress upon your son the importance of an upward trajectory for ALL the colleges on his list.
Your son must redouble his efforts the second semester. And, he should have a conversation with his guidance counselor now and ask them what they recommend. One possible solution: If your son improves his grades during the first making period of the second semester, his GC might be able to send those grades to all the colleges on his list (not just to Yale).