Then again, we're talking about a people who hunted a harmless fish to near extinction, simply because it somewhat resembles a dragon. (See Fishing Log text for Leafy Seadragon.) The Ishgardians haven't really demonstrated that they show a lot of finesse in deciding which dragonlike things are to be killed on sight and which are A-OK. XD
I have the feeling, though, that even if Ishgardians show enmity toward Au Ra in general, they'll treat Au Ra adventurers the same as any other, just like Duskwights and Keepers of the Moon adventurers aren't given any crap in Gridania in spite of the prejudice against them there.
