The controller was still 'in control' and able to intervene instantly if anything somehow went wrong (different scenario altogether to placing a child in the 'driver's seat' and standing behind him or her). Therefore, risk of an incident was minimal to none.
The guy is probably excellent at his job or at least must be reasonably competent to be allowed to work there in the first place. If he loses his job all that ability and experience (and money spent on training him) is wasted.
However, he displayed a bizarre lack of common sense and foresight (as did his supervisor) by not seeing what was coming - it wasn't what he is trained to look out for but he should have seen it anyway. Air traffic controllers should have an awareness of risk factors after all.
JFK ATC does not live in a vacuum. Even if none of the other controllers or pilots who heard the transmissions ever made mention of it (either critically or as just a point of interest) there are plenty of other people who could be listening in either directly or online so it was going to become a subject of conversation at some point.
There was then no way in the world that someone in the media, somewhere, was not going to pick up the story and run amok with it. Newspapers and TV, let alone the Internet, are full of even less worthy stories than this that get the headline "shock, horror" treatment so it was going to happen and when it did the knee jerk reaction from the bosses was totally inevitable.
They have backsides to protect as well and didn't get where they are today by showing backbone and supporting their staff in the face of pressure from the media and 'public opinion' (whatever that is). You don't get to high places in bureaucratic bodies by displaying those sort of qualities!
My problem with the judgement skills of the guy at the centre of the storm isn't that he endangered anyone else but that he voluntarily put himself so firmly in the firing line. We all make bad judgement calls (I have made some beauties in my time and still do) but do it publicly (and, like it or not, JFK Tower is not exactly Top Secret) and you've got to expect the flak to find you. You are kidding yourself if you think it won't.
I hope wisdom prevails and after a serious chat about the perils of stirring the media and perhaps some training in personal risk assessment, he and his supervisor are allowed to continue their careers once the storm has died down.
I hope eventually his kids learn some useful lessons from the episode as well - but I'm not too confident that so far they have - and if Dad gets sacked then the (totally unjustified) feelings of guilt will be enormous - not healthy at all and something all the adults involved would do well to consider seriously.