For serious. Magneto's own series spells it out clear as day for him that part of Charles was still in there.
Magneto maybe doubted that this part of Xavier could be rescued or brought to the forefront, but he wasn't unaware of it.
I still say Magneto's choice to kill the Skull was the right call since he didn't know what was going to happen, had no reason to believe Charles could be extracted, and had to stop an imminent threat to the whole world -- but it is good for the character that he is exhibiting regret.