The ends does not justify the means.
What Xehanort does throughout the series, what actions he takes in order to try to recreate reality and bring back lost friends is in and of themselves evil. Even though he's a sympathetic villain just wanting to see the friends that he lost in the past (aka dark road), the extremes he takes are at the detriment or destruction of others.
Forcefully taking over Terra's body for the sake of leaving his old frail body behind in order to live longer.
Striking down his only living friend (Eraqus).
Kidnapping a 4 year old girl (Kairi) and doing experiments on her against her will.
Splitting his pupil's heart almost killing him (Ven).
Tries to possess a 15 year olds body just to have complete control of him (Sora).
Tells his subordinate (Vanitas) to "kill" Aqua.
The list goes on. Dude's evil.