Aela Talith
The Righteous
Perhaps the biggest, and most important quesiton with an organization like the SIS is oversight.
Who watches the watchers?
The simplest, and most honest answers is they do. The Strategic Intelligence Service in it's current form is made up of people from all over the galaxy, men, women, humans, and aliens all have a part. Though the Director is the head of the Organization, the Mandate of the SIS demands that the Agency does good. If any Agent feels there is a conflict of that mandate, they can, and should raise the issue.
The Agency keeps itself in check through the collective morality of those working for it.
Every single person within the SIS has a voice, and they are more than inclined to use it for the good of the Galaxy.