To my understanding, before garlemald came along and issued their ultimatum to kick out beastmen and those with the echo things were generally on better terms between the races of eorzea outside of the ixal's logging and the sahagin and pirates fighting each other on the seas.

But even then, the only peoples kicked out and brought to conflict were those races that had summoned primals over the course of 1.0. Qiqirn, Mamool Ja, and Lupin have not and are treated like anyone else.