Don't freak out!
This is from Yale's website (specifically the FAQ section......Also, I'm impressed with myself that I remembered this nearly verbatim....anywhoo):
I was very sick first semester of junior year, and my grades suffered. Once I recovered, my grades improved. How can I let Yale know about my special circumstances?
Ask your guidance counselor to address any special circumstances in his or her letter. Some students also choose to write about particular challenges in their personal statements, but it is always a good idea to have your counselor explain the situation.
In any case, what you did was absolutely legitimate: You provided Yale with additional information where you felt it was necessary.