So I used the level up cheat on some of my soldiers and so I was able to send them on the covert missions where you locate the stronghold that the assassin is in. And so I killed the assassin much earlier in the game then you are expected to. After that I did the mission where you rescue Mox and as the mission ends the assassin talks to you but of course how can she be talking to me when I killed her and the answer is because it is a scripted event.
I don't think you broke it by "cheating".
I recently unlocked the mission in her stronghold but I (had to do a lot...) never made the rescue Mox mission so far. The mission is no "need" to it's just not planned I guess that someone pushes a free character that far out.