That's not quite accurate. In BKV's run when it was mentioned that she slit Banshee's throat she flatly denied it and claimed it must have been someone else, but it was never clear whether she was telling the truth or just tossing off a quick denial.
If I recall correctly, Moira's death was mentioned in another X-title and put down to Mystique having an utter breakdown after the death of Destiny. She certainly went through a stage of unrepenting villainy, though, which got back to more shades of gray with BKV's Mystique solo title.
I personally think BKV tossed that line into the script so people could claim it their personal canon that there was a duplicate Mystique out there responsible for that period of writing. I don't believe that there were any solid plans to reveal that to be true or a storyline involving it, just a nod towards those who found her going from being written as a pure villain to being more a more sympathetic character again in her solo title jarring.