R. Star wrote:
The difference between Section 31 and the CIA, is the CIA is ultimately answerable to the government of the US. Section 31 is not answerable in any way to Starfleet or the Federation government. That's the morality of it in a nutshell, lack of accountability.
This can be a positive. It allows the organization to do things that the Federation, with its high ideals would not sanction...while officially being independent of the Federation itself. This includes the virus, summary execution of the treasonous President, as well as getting Koval to there side (violates prime directive of noninterference).
The unaccountability and independence is a clever backdoor in the Federation Charter.