The Guardian Council is the small team of elite Guardians who control and direct the Guardian's organization. Due to the size of the Council, it appears to be formed somewhat like a Governmental Cabinet.
The council is lead by the Prime Guardian, currently Turbo. It is unknown exactly how many Guardians serve on the council, but at least four have been observed at a council meeting.
The Guardian Council's overall aims seem to be quite clear - when virus-free; protect the known Net at all costs. However their methods vary from hands-off approaches to systematic purges to protect the greater good. This would seem to put the Council methods firmly in the grounds of "The Ends justify the Means".
The Council has a standing policy that if a Web Creature is found in any small system on the Net, the system will be sacrificed in order to destroy the creature, to keep it from spreading to the rest of the Net.
The Council decides things by voting. During the Web War in Mainframe, the Council came to agreement on what they had to do about it. It can be presumed that entrance to the Council is gained on a merit and promotional basis. As Turbo seemingly educated Bob when Bob was graduating at the Guardian Academy, it would seem that Turbo has served as a Guardian for a significant amount of time, explaining his position as Prime Guardian. (Trust No One)
It is possible that Daecon was a member of the Guardian Council, since he became Daemon's advisor when the system was infected.
Turbo latter claimed that Daemon let the Web Creature into Mainframe. The Guardian Council's decision to destroy Mainframe is still most likely a decision free of the viral infection. Possibly releasing the Web Creature was meant as a distraction while Daemon took over. (The Episode With No Name)