Well, akshually, the word has multiple meanings. It's both the male name Aquila (masculine nominative) and
eagle or
legion standard (both feminine nominative, the latter by metonymic expansion – the banners were topped with eagle statues).
Here's the thing, though: Roman women did not normally bear any individualizing first names ('
cognomia') and most women during the Republic had only their father's gentile name (a surname of sorts) in the feminine form (which, for Aquila, is also Aquila – though occasionally Aquilaria in the genitive).
Also: a) the game is not set in ancient Rome; b) modernly, Aquila has, in some places, been used as a female name (things and languages change); and c) Aquila is just a badass name. So, all in all, thumbs up. Also, I should be working.
Edit:
The only famous (Ancient) Roman using Aquila I've heard of was Marcus Flavius Aquila but his actual name was just Marcus Flavius. Aquila was added to the end as an honorary since he was the one who recovered the lost standard of the 9th Legion. Thus, he became known as Marcus Flavious "The Eagle". I couldn't find an instance of someone named Aquila before him. After him you can find Aquila used as both given name and surname so, he might have been the first. That's just from a bit of google research so, far from a scholarly opinion.
Aquila was both a cognomen (v.g., Aquila Romanus, grammarian) and a gentile name (v.g., Pontius Aquila, tribune).
