Is he protected, or was he using Starfleet personnel for his own ends? I don’t recall that it ever explicitly shows them officially working together. With Inter Arnim Selim Legis, the Admiral is working with Sloan, not for him or commanding him. A relationship of convenience, not an official one. Similar to when they’re looking for the cure for Odo, it’s not specific people working directly for Section 31, just people who are either working with them out of convenience… or being manipulated similar to Bashir and the Admiral whose name I can’t remember from the aforementioned episode.
That doesn’t speak to an official relationship, just the manipulative one of a parasitic organism pretending to be a mutualistic one.