Okay, I know this is ollllld but I only just saw the episode.
Wow. Sucked. Not because I'm against CIs, but it just didn't ring true at all. And yes I know it's a sitcom, but when Scrubs isn't doing the fantasy thing, they do often come up with realistic scenarios. I think this was clearly written by someone who knew just a little bit about CIs and had no input from anyone in the deaf community. As mentioned, the process of getting the kid the operation was not at all realistic and how is J.D. qualified to just look at the chart and figure out that the boy was a candidate? He's not an audiologist.
And culturally it was just weird. The father is obviously Deaf and just caves when a couple of doctors push him on the issue? Ridiculous.
They made it seem like getting a CI is some kind of lifesaving operation that it is simply medically wrong not to approve for your child (even going so far as to suggest it's child abuse NOT to implant your child). I don't think the writers did much research into the subject whatsoever.
I watched this right after seeing the Law & Order: Criminal Intent episode about the deaf activists and I have to say, major kudos to NBC for employing so many d/Deaf actors and signers...but do they ever need to work on their scripts.