The name Section 31 is literally derived from Section 31, Article 14 of the Starfleet Charter which authorizes the complete and total abandonment of any and all Starfleet regulations in a time of crisis.
And this is where I point out that the charter in question is that of the EARTH Starfleet, not the Federation Starfleet (the two are not the same organization).
So even if Section 31 was justified in ENT's time, it would be null and void by the formation of the Federation.