It is a matter of public record that the SEC was sent a detailed study on the likelihood that Madoff was running a "Ponzi scheme," yet they chose to do nothing.
As for the first point, it is totally up to them to keep quiet about Madoff's problem. However, this opens the possibility that there are whole lot of crooks they knew but kept quiet about.
We already know that these institutions are not good apples. There are other bad apples not outted yet but whom they know about. The whole place was pretty sinister, Byzantine web of deception and fraud. Nothing was what it is supposed to be. Transparency was and is far from their concern.
They were free to make their decision, but their decision are now poisoning the credibility of the whole industry.