The actual wording in Inquisition is that Section 31 was part of the original Starfleet charter, therefore no reason why they couldn't be around in ENT.
I still think it's a retcon, as the wording in DS9 was obviously referring to the Federation Starfleet, since the idea of an Earth Starfleet didn't exist yet.
And we saw some associates of Sloan on the holodeck in "In the Cards". But since that was a holodeck, there's no particular reason to think they ever really existed.
Indeed, there's fairly little reason to think S31 exists, either. Sloan sounds like a madman; if he was a disgruntled, traumatized or otherwise silly ex-SFI agent and happened to own a boat with a transporter and a holodeck, he'd be able to pull off everything we saw in DS9.
S31 might have existed back in ENT, with real organization, operatives and whatnot. Two centuries later, people claiming to be from that organization would more probably be lone nutcases than not...
Timo Saloniemi
Yeah, I wish that would have been the case, but that obviously wasn't the intention.
The interesting thing is that my wife and I are doing a Babylon 5 rewatch, and I'm noticing that Section 31 bears an
awfully strong resemblance to the Psi Corps. Even to the point where Bester comments to Garibaldi that there are threats that Earth has faced that the general public no nothing about because the Corps stopped them before they could do anything. Heck, they even had the evil black uniforms. But of course the Psi Corps came before Section 31, so...