Individuals can't do things like this without an organization.

If an organization murders someone, who serves the punishment? You can't put an organization in prison, though you could shut it down for a period of years. Or you assign guilt to specific people and put them in prison.

We've got to get better at "piercing the corporate veil."

There's somewhat of a breakdown between responsibility and criminal liability, and you've jumped from one to the other. The original comment was talking about responsibility, and in this sense, an organisation's internal practices, accepted behaviours etc. all share significantly in the responsibility. Often responsibility really is impersonal. On the other hand, the substance of your comment points to the fact that criminal law is served on an individual basis, and perhaps that's a good thing.

It is, however, ignorant at best if we stop discussion completely at the point where an individual is put in prison for something they did on behalf of the organisation, or due to organisation policy etc. since part of the justice system is deterrence, the organisation itself should be factored into that calculation.

Various mafias are also organisations, but that's a much easier case than this - shut down a mafia by taking the heads of the organisation. That works because it's not "just business". But in the case of MIT I have a strong feeling that if there is such a systemic issue as other commenters are hinting towards, it won't be so easy to be rid of it by putting the person in top position in prison. Such a person is the appearance, not the essence.

Is this a Foucault meme?

I think I agree with you, but I've seen people make similar statements without elaboration and feel I may be missing some important subtext.