Well, I have multiple ideas for how it could work. One of those being that while Damian is in line to inherit Ra's Al Ghul's position as the head of his organization as a whole like, as the next Demon's head for the sake of metaphor the League of Assassins often has a separate subordinate leader running it who's supposed to be loyal to Ra's and protect him and his organization since they're the Demon's Fang that protects the head in the whole weird analogy (see Doctor Dark, The Sensei etc, granted most of them betrayed Ra's at some point but still) 

So depending on your interpretation of how The League of Assassins works, even though Talia and Damian are meant to control the whole thing including both the League and all the criminal/financial/political stuff separate from the League everyone forgets about, Cassandra could still have been in control of the League of Assassins itself with Ra's blessing and been given more than some autonomy to do so. Actually I'm almost thinking she was specifically created to serve in that capacity hence Ra's suggesting David Cain create The One Who is All in the first place, or at least that's how I thought it was in some interpretations. Also explains why the assassins would follow "some kid" they've never met before since she was a project specifically meant to create the perfect capital A Assassin to loyally serve The Demon's Head, even if it took much longer and a little bit of brainwashing to get there. (Also kind of explains Damian being under the Character Impression that she resents him because she was created to serve him).

So, she could be the leader of the League with them around without it being a conflict of interest or out of character. That's just one idea though, if you don't like it or feel like it doesn't work I have some other ideas. Keep in mind I'm running on lack of sleep.