Unless there is a setting I haven't found yet (VERY possible) Carbonite shows every flight master on the map (in case that's why you went there). Regardless of their, or your, affiliation.
Carbonite has no way of knowing whether the Scryers, or the Aldor, will kill you on sight. It's the same for Booty Bay, Gadgetzan, the Oracles, the Frenzyheart, and other factions you can lose reputation with (or just start off as Hated).