Her eyes have nothing to do with it. The reason she is in involved in mortal politics simply ruins the Volkihar and makes them carbon copies of the Cyrodiilic clan. The Blue Palace, a place of Imperial power, should have a member of the Order and not a Volkihar. Illusion magic has nothing to do with it. The fact that she looked human, like Alva, like Movarth gave us the impression she was a member of the Order. Dawnguard changed this when her face was changed and her dialogue was tweaked.
Personally, Volkihar should stick to their courthouse of freaks in their own Draculian-style and not stick their bat-noses into politics not of their own. The last thing we need is a clan of savage blood-svcking fiends who can't so much as blend in without enthralling people rather than taking their daily dose of sanguine and going about their lives. We need a diversity in tribes. The Volkihar, while sharing some traits of the Order, I.E, feeding on sleeping people(also prisoners), having a hatred of thin-bloods and barbaric cave dwelling monsters, and having their own "organized" group and worshiping Bal, should be different when it comes to goals and tactics.
The fact that the vanilla ones were changed is peeving. Stage 4 attacks was there for a good reason. While the physical apperance did not change no matter how much you fed, it was heavily implied that feeding diminished the preternatural condition of the character. Otherwise why would people "recognize" you as a blood-starved vamp in the first place? With Dawnguard, they removed this and added bat-faced vamps and no stage 4 attacks with the additional people who can recognize your vampirism such as the face changer in Riften.
By gameplay reasons, people do not attack you now no matter how long you went without feeding. But this is gameplay mechanics. In "reality", I am quite sure a glowing eyed, fanged individual would be attacked on sight. Yet it doesn't happen in the game anymore unless the player sprouts wings and looks like a half-bat monstrosity. By all means, Volkihar are the gangrel creatures who cannot change their apperarance or blend in unless using illusion spells(I know, I said illusion has nothing to do with it. What I meant is Sybille could not go around casting seduction spells on every member of the Blue Palace . . .it wouldn't make any sense.)
Or the truth is Bethesda simply applied a change to all vampiric NPCs and you're trying desperately to make up some fan lore to make sense of it.
Why can't people just admit Bethesda dropped the ball with vampires in Skyrim?
Shirnos is a massive Volkihar fan. The idea that Sybille is a member of the Order is insulting his favorite tribe.