Mystique may have been a villain in the X-Men comics and early X-Men movies, but the “First Class” series has charted her growing into a her.
But this also means that Mystique’s story can properly conclude, allowing Lawrence to leave the world of mutants and continue along with her Hollywood career elsewhere.
So the corrupted Jean Grey killing her would be a tragic and emotionally-wrenching end for her since she’s likely formed a bond with Jean by that point.
It’s a reasonable explanation, but that doesn’t ruled out Mystique being killed.