I kept an Evernote notebook of medical articles about OCD. The reviews of the operation your son had (I believe it is called Osteochondral Autograft Transfer or OAT) are very good. The studies show that he should be able to throw without pain in 6 months, and he should return to playing baseball at the same level after full rehabilitation. From what I have read, his operation sounds normal. The OAT procedure involves a little more pain because 2 joints are being operated on. The hardest part is now over and he can look forward to getting back to normal!
Do you know the size of his lesion and whether it extended to the margin of the cartilage? From what I have read, it is performed on larger lesions or ones that are not completely surrounded by cartilage. As my son's was relatively small, the recommended procedure for him was the debridement and microfracture.
I hope that he is feeling better and is now on the road to full recovery.