Everything you just claimed above about S31 has at one time or another been attributed to the various spy agencies who spy on each other as well as their own people, nobody trusts anyone in the spy game especially not their own populations, its one of the reasons 9/11 occurred, if the various agencies had actually talked to each other and shared intel it could have been stopped.
Real people can be power hungry and operate outside of the law with the best of intentions (or not), not just those we see on the TV screen or at the cinema, its not about the black and white its all about the shades of grey in between.
Even today there are black budgets/operations and many things we aren't told about just like during the cold war, this isn't paranoia on my part its just common sense.