Aren't they heavily implying that it's Mystique, getting her revenge for Xavier & Magneto denying Destiny's resurrection?
The real twist would be if Magneto was the murderer after all.
That I don't know. I don't follow all the X-titles, so if there have been scenes that imply Mystique outside of the X-Men title I haven't seen them.
I hate Mystique as a character so much with her stupid impractical dress and this idea that she can biologically morph into clothes or armor. I also hate how the movies raised her profile so she's around all the time, and that they put her on the Council even though they are actively ruining her life and also the fact that she is a murderous terrorist who's betrayed them over and over again.
I picked up X-Factor 10 and X-Corp 2 and that confirmed for me that I am glad I never tried to follow all the X-titles.