Yes, it was revealed that people like Admiral Cartwright, Colonel West, and Valeris were at least working in concert with a Section 31 operation.
Although, it makes less sense for it to be an S31 operation, seeing that they tried to end the Dominion War more quickly with the Founder Virus, and wanted to delay a war between Earth and Romulus for as long as possible.
The entire Insurrection story seemed like a perfect S31 operation as well, and it was later revealed in a ST novel that this was the case.
IIRC, at first on ENT the organization was just referred to as 'the agency', but we later learned that this was clearly Section 31, after Harris mentioned that it was in the United Earth Charter Article 14, Section 31 (or was it the Starfleet Charter?).