Update: landed at JFK and just got off the phone with PM line. Explained the situation to the agent (who was great btw) and he got his supervisor involved. After holding for about 15 min he came back apologizing staying that the GA was wrong. Supervisor spoke to GA in question and clarified policy with her and upgraded me in advance to J for my return flight on Monday. I asked for and was granted 2 $150 vouchers which was the approx difference between lowest fare and K at time of purchase.

In the end I feel like Delta made right on their error, but the situation was still frustrating.