A clear distinction is made between Pureblood Garleans who identify as Imperials and those who do not. We've also seen multiple Pureblood Garlean NPC's and conscripts defect and readily work with the Eorzean Alliance with little to no outright discrimination involved. Given that we already see the likes of Cid and Nero frequently save the day for Eorzea from as early as ARR and many more times beyond that point...I have my doubts that it's the red line that some people are painting it as.

The player character is already a special snowflake on many potential fronts. Many circumstances of which are roughly equal to the idea of being a Garlean Pureblood who just so happens to be able to be one of the few capable of wielding aether.

I get that some people are worried that they might be super popular and that there would be many of them throughout the game world as a result but I, personally, don't believe that the player character makeup needs to reflect the rarity of supposed lore restrictions.