I loathe the NY Times. I don't like their staff. They are the voice of most of what's wrong with the US. They are liberal/socialist shills.
Their actions on this matter are reprehensible.
But what the NY Times has done is perfectly legal. And constitutionally protected. They are afforded the same right to free speech as the rest of us.
The people that need to be dealt with are those that are apparently compromising classified information for political means (and yes, it's purely political). There are moles in the government and they do need to be prosecuted.