I do imagine Section 31 operating like a terrorist cell, like the organization detailed in the movie Battle of Algiers. So if one person is captured, all they know about is their direct superior and their direct inferiors.
How do we know the things Section 31 has done other than trying to wipe out the Founders and putting Federation sympathizers in Romulan positions of power? They must be competent because they haven't been discovered, but how do you know they weren't, for instance, behind Admiral Lleyton's assignment?
And, you're totally right about Cerberus but I'm speaking more of what they appeared to be in the second game. I believe, for instance, that they absolutely would run medical tests on people against their will in order to cure diseases or engineer biological weapons. They would rather capture a weapon of mass destruction than destroy it.