When was the Empire "kill them all"? They conquer by the sword, absolutely, but clearly entreat peaceful submission. I've read enough imperial banter to consider it quite obvious that any nation-state offering to be a imperial principality enters the Empire on far, far better terms than one that gets crushed into joining. The Empire from our character's perspective is, to be frank, butthurt enough to be vindictive at the constant failures they've had trying to extend themselves into Eorzea.

Without spoiling too much for anyone, the aversion or deficiency of pure blooded imperials to touch and use aether as magic may quite possibly render them dull to the influence of primals. I have no doubt this will be a critical plot point, moving forward.

I also have no doubt that future expansions will take us into the imperial cities - and I have no doubt you'll find them prosperous, probably even pleasant, although strict. My reasoning for this is fairly simple: The Imperials are modeled after the Roman Empire, plain as day. Being a Roman citizen was pretty much the best deal around for its time, and during the peak of the Roman Empire, acceptance for citizenship was an immensely coveted thing.