Just because a one size fits all rig works for one developer doesn't mean it does from another. I really don't appreciate the naivete of some developers saying, "Well this should be easy!" without any understanding of the work pipelines for the specific engine being used. I've worked for Ubi and for them it's going to be a whole new set of mo-capped animations, etc. It's a bit more than a drop in the hat.
All that said, the realities of the situation are as follows:
1) They should have been upfront with their reasons. Games are a creative endeavor. If they don't want to include a female assassin for a narrative reason, just say, "We didn't feel that a female assassin fit the narrative we were trying to tell." Still going to get backlash there, sure, but I agree with some of the other posters in this thread that have made the argument of it being ridiculous to 'require' there to be a female character.
2) It likely wasn't narrative, but instead an assessment of cost/benefit analysis and swinging the pendulum too far. Nothing more, nothing less. AC sells to a predominantly male demographic. Let's not forget that Ubi did have an AC title with an African American Female protagonist. It was also the worst selling in the entire franchise, despite an HD re-release on multiple platforms. If there was talk of a female assassin, it was likely shot down with sales figures and survey data. Not saying its right, not saying it was a good choice, but if I had to made an educated guess as to why, it's this.