Well, reading Marcus' letter I got the idea that Marcus implied that she was killed when they fled away.
Well, Marcus job as guardian was to protect MC's noble family from harm. So it's not wrong or full of him to assume "those people" killed her where he wasn't around to protect her. And with the death of his beloved it's easier for him to stay focused on the given task, not trying to find out if that's true, not trying to save her.
But there is no evidence it's true, only Marcus assumptions. The truth could be way worst than that. Like, for example, MC's mom not being dead, but being held in a dungeon and constantly being tortured, raped and rejuvenated by magic/alchemy to give the information about her child.
But looking at Chyos work I'm sure on 69,34% she's dead, because by being dead she won't require too much of work, won't spoil too much of MC's orgins by answering his questions, which is one of the main plotlines in the game.
On the other hand, or at least somewhat on 34,69%, she may be alive waiting for MC's to fuck her, because patrons may want and vote to have her like that and Chyos will make it work somehow.