Our characters are evil, main quest proves it.

[Enkidoh]

Ifrit was just referring to the Echo and how it protects the player from a Primal's influence (because it's come from a power even higher than them, ala, the Mothercrystal). The Echo was given to the player with no evil intent, even if does still make us pawns of a higher power, it's a kind of 'end justifies the means' thing (because the Mothercrystal is the source of all life on the planet, if it was to be destroyed, well, it should be obvious just what a bad idea that would be). And the Echo does prove extremely useful to the player in their travels, so it's not exactly an unwelcome ability to have.

Eorzeans only wanted to be left in peace - the Empire are the ones with delusions of grandeur and are hellbent on planet-wide conquest. So this idea that the Empire are just misguided and that we're the evil ones is not only a rather convoluted, it comes across as more wishful thinking from players who have just spent far too much time playing GTA and want a RPG where they can be the 'bad guy' so to speak, no matter how ridiculous such a concept would be in a FF title.