So is the deleted scene canon or not?
On X-Men Wiki it is considered canon, and reads as follows:
"About a month after the Missile Crisis, Moira and Xavier have fallen in love with each other, and she is caring for the wheelchair-bound Xavier at his mansion. Moira, who normally wears formal clothing or pants, has donned more attractive feminine clothing. She is wearing a sexy dress with a short skirt, revealing her thin shapely legs and highlighting her incredible bosom. She and Xavier talk about his School, and she calls Xavier and his pupils "X-Men." Xavier then tells her that the schools will require anonymity. Moira tells him sexily that she will never tell the location of his school to the CIA, no matter how much they interrogate her. He tells her that he knows, but it is clear that he does not believe her to be reliable, despite their deep love for each other. He then passionately kisses her, during which he erases her memory as a safeguard measure to prevent her from being effectively interviewed by her superiors.. The scene then cuts to sometime later with Moira being interviewed by her superiors at the CIA. She says that she remembers the attack on headquarters, leaving to go somewhere else, and then waking up this morning. Her boss is stunned by this and asks if she really cannot remember anything. She says that she recalls "fragments," such as trees, sunlight, and the kiss, at which point her eyes drift off, and she smiles dreamily like an amorous schoolgirl. Her superiors are exasperated by this and conclude that that is why a woman should not be in the CIA. Lehnsherr and his fellow mutants then invade the CIA headquarters to free and recruit the imprisoned Frost."
I believe it's safe to say that the sense that I picked up during those scenes, including the beach scene, were meant to show that there was something there between Charles and Moira, afterall, they did (per this scene defined above) fall in love!
