She's evil, and wicked, and villainous and every other synonym to that effect, both in his eyes and in the eyes of the people. But Merlin, for all the distance in between them, still understands her better than anyone in the world, even Morgause. Because Merlin knows her heart, broken and twisted and damaged beyond repair, and he understands her suffering and you cannot hate that which you understand so well, only pity it and lament what could have been.
And as he stares across the battlefield, his memory filled with images of Arthur and Gwen, Merlin thinks that Morgana Le Fay is still the most beautiful girl in the world.