So Mystique doesn't know Rogue at all? Because it's pretty goddamn easy to see she wouldn't want to even risk the life of the baby to save herself. Gambit even says as much. So either Mystique didn't care what Rogue wanted or she doesn't know her "beloved" daughter at all.
And the way Mystique hides whats she's going to to do with the baby from Gambit led me to believe it along with the way she tells Rogue it's still alive like even she didn't expect it. And even if she didn't expect the child to die she still orchestrated events that resulted in multiple other deaths to get the child which Rogue herself calls her on.