First of all:In real life the Aquila is a Roman symbol. Used by Germany because they heavily identify with the Romans, and have done so since the middle aged (See the Holy Roman Empire, which is not actually Roman)
Second of all: The eagle used by the Germans in WWII is completely different.
The Nazi Eagle Emblem has an eagle holding onto a wreath with the inverted Hindu Peace Symbol.
The Imperial Aquila is a double headed eagle. The head looking to the left is ever watchful of herasy while the head looking to the right is blind (Hence the lack of an eye) to the necessary evil committed by the Imperium (yknow, so that everybody doesn't get their souls eaten by demons and or tyranids).
Thirdly... I'm not even going to try to defend the horrible pun that is her name...