Is MIT being hypocritical? Clearly not since what they are saying and and what they are doing in this case do not appear to be at odds with each other. It would by hypocritical if they, for example, both supported the students verbally, but at the same time encouraged the prosecution in some way.

I think you meant to suggest they were being inconsistent here. Or perhaps suggesting they were applying a double standard. If the former then (given the poor way they handled the Swartz affair) that is to be welcomed. If the latter then I suspect there are enough differences to suggest that a different approach is indeed warranted.

You go on to suggest that the different reaction to this case on the part of MIT is perhaps a cynical PR exercise while at the same time berating them for the poor handling of the Swartz event. Is it not perhaps an alternative that they have taken the public reaction to heart and have changed in their outlook? Indeed, now that they take a more positive reaction you criticize them for changing.

While their treatment of Swartz was appalling, that's no reason to insist they behave like that in all cases - and less reason for complaining when they improve.