Personally, I thought that the dragons came over from Dravania instead; look at the map of Eorzea, and you see a huge dragon floating about in the north-western area of the main continent.

My view is that Ishgard was not necessarily present at the time at all; a class-quest for CON mentions that Ishgardians loathe dragons, to the point at alerting higher-ranks that Gridania was 'hiding' dragons. I would think that the city of Mor Dhona was an innocent city which got caught up in the middle between the war of the Garlean Empire and dragons, and got destroyed when the dragon decided to land and crash the airships over it. The remnants and survivors of the incident migrated north to the relatively short distance-away Coerthas, established Ishgard, and bear a hatred to the dragons for causing the harm to their beloved town.

Of course, this is all mere speculation but...