It sounds like to me, that Ubisoft never planned on having one of the characters be female (initially), and then at some point they went back to review that decision and decided it was too late to change it. If that's the case, then yes, time and money are definitely justifiable reasons. You have to hire a new VA and re-record all their lines (with possibly rewriting the script and having the other voice actors redo any and all lines affected by the change in gender), redesign the character and their alternate outfits, go through all of that characters animations and adjust them to work with the new character....and remember that these are extremely detailed characters/animations now, so we aren't just talking about swapping out a model - there really is a lot to consider here.
I'm all for having female characters in games (when given the option to choose a character's sex, I almost always pick female for one if not my only play-throughs, if only for a good change of pace), but I am against forcing gender, age, race, or sexual orientation into games, film and other forms of art. If a company decides that their protagonists are all man, or all female, fine. That is entirely their prerogative and I think it's horrifyingly plebeian of people to automatically jump in with the sexist card and/or demand that a company or artist change their work to fit someone else's view of world. Would it be cool to have one of the characters be female? SURE! Does it make Ubisoft sexiest that there is not a female character? NO!