I don't remember a scene that had Charles & Mystique together in any of the three movies.
They didn't have too.
She tried to murder him using Cerebro in X-Men 1.
That's some gratitude for taking her in and caring for her all those years, huh?
Hell hath no fury like a woman scorned...
...and, apparently, Mystique got scorned a lot, havin' to watch Xavier hit on women at the bar all the time, and then bein' rejected by him when she was blue, nude & feelin' vulnerable.
So her plan is to help murder him because of his personal preference in women from decades ago?
That doesn't make any sense, especially since their was no sexual innuendo or tension between them to imply any attraction.
That's not a scorned woman, that's a psycho.
I can't blame Charles for being morally and ethically sound in not wanting to see the women he grew up calling "sister" in the nude or beaten to death by the human public for being blue.
Mystique knew this too according to X-Men 1, her own parents tried to kill her for being born blue & nude.