That would've been the case, had she gotten away with it
Yep. It all came down to her killing him AND being caught. They needed her to parade to the world and they needed her DNA to perfect the Sentinels. Charles acted like it was all about convincing Mystique to not kill but Magneto was on the right track as well in recognizing that as long as she didn't get caught that would also prevent the Sentinel uprising.
What I'd like to know is how did Magneto take control of the Sentinels. At first I thought he was using the metal that he intertwined with their endoskeletons to manipulate them like puppets but clearly he was in control of their every thought and function for a time. How did he manage that?