I don't know the precise nature of the co-op, but in co-op I don't see why they can't give the option to play as a girl. I don't care if it doesn't fit with the story.
I'll break it down for you because you really don't seem to know that much about this game or the series in the first place.
1.AC games have always had a set narrative, a main character with a backstory, personality, character development etc
2.AC games have always taken place during historical periods. The point is that we're supposed to believe that these characters actually existed and actually affected history during their respective time periods. In other words, it's historical fiction.
3.AC games, particularly this one, have ALWAYS had one main playable character during the of the games with few exceptions.
4.Thanks to next gen consoles and the popularity of games like Dark Souls, things like seamless multiplayer is becoming popular.
5.Seamless multiplayer is one of the best things in Watch Dogs, when people come into your game to play with you, it's all seamless. They see themselves as the main character. You see yourself as the main character. They see YOU as an generic npc. They can't see themselves as anyone other than the main character. A downside of this is that it looks awkward when some npcs like a chubby women is using the same animations as a the main character who is a fit male. This includes parkour moves and melee combat.
6.In ACUnity, they're for the first time incorporating seamless multiplayer into the series SP. And like in Watch Dogs, YOU always see yourself as the main character. However, they go one step further and allow you to customize your gear, which includes weapons, outfits, skill points etc, which is also a first for the series.
7.The animation quality bar is at an all time high for the series in ACUnity.
8.In AC games the environments were created in a 1:3 scale, in AC Unity, thanks to next gen only development, they were able to create the buildings in 1:1 scale.
9.Due to the 1:1 scale, they had to complete revamp nearly every aspect of the game.
10.So developers created 8000+ new animations for the main character alone
11.Now back to multiplayer integration. During the multiplayer, you can the outfits and gear that players chose to wear/use in their game.
12.To keep the quality of the animation at the all time high that I mentioned earlier, they decided to just swap out the face of the character that you see your friends as.
13.If they would have created a female face, it would look awkward like in Watch Dogs because they were all specifically created for the MC, who is a male with a set narrative. The series does not allow you to change your gender because it's not an rpg like Mass Effect
14.Not only that, but this game has a 2014 release date and has been in development for three years. They would've had to either lower the quality of the female animations, or create ones at the same high bar as the MC. That's just not possible with the time.
15.The kicker is that the person playing would never be aware that they would be playing as a female in the first place. Meaning that the effort involved in a female character and somehow creating technology where the player has different animations onscreen than what other players see is just no worth it. Nor does it have any benefits besides a pat on the back from people who most likely weren't as excited for the game as the fans of the game/a very small increase in sales.