Also, provided that "an intolerable threat to the security of the Federation" does translate into some level of Federation or Starfleet legalese, it's possible that, once the Maquis were classified in such a manner, Sisko did
have the authority, or at least the potential authority, to "gas" the colony (which IMO implies a bit more than actually occurred; i.e. it seems like a weasel-word). It may have been at the extreme end of what Sisko was allowed to do, or it may have been well within the range, but not commonly invoked. Hell, for all we know at that point Sisko might have been able to get away with nuking the planet.
In any case, notably none of the Defiant
crew actually made a move to belay Sisko's order, which effectively would make them all guilty. The fact that none of them actually opposed it could be construed as indicating that Sisko did
have the authority to issue the orders he issued at that point in time. As I said, perhaps they were surprised because the order was a possibility but not generally pursued, or perhaps they initially thought he was bluffing and were surprised to find out that wasn't the case.