I think we can go back to the point that though they have horns they are unlikely to be anything like the Ishgardians have seen from the Dravanians before and if they prove themselves enemies of the Dragons they are less likely to care. The Ishgardians are paranoid towards anyone who isn't from Ishgard. The most zealot of the lot probably see all outsiders as heretics anyway.

More to the point, while the WoL is heading to Ishgard for shelter, Ishgard is pretty desperately in need of aid and aren't quite in the position to be turning away help at this point. There defences are all but striped away and even holding that forced them to rely on sellswords and adventurers. Its hardly like that one battle has won the war for Ishgard. It won one battle but at the cost of much of its defences. The dragons are still on the offensive since Ishgard has been forced to pull almost all its forces back inside Ishgard to protect the city.