Of course he loved her.
Although he had never been particularly good at being honest with himself, it was harder to argue with a manifestation of your darker side than it was to argue with that little voice in the back of the head which would shut up with some good prodding. The Dream Lord had gone beyond implying it to blatantly stating it: the Doctor loved Amelia Jessica Pond.
He fell in love far too often, he sometimes thought. Rose was the obvious case. River sprang to mind, though that hadn't – or possibly had – happened yet. And now Amy.
Ah, but the Doctor had learnt his lesson. He had seen Rose decide to leave him without realising that was what she was deciding; he had seen River sacrifice herself for the sake of their future. He wouldn't give Amy the opportunity; he wouldn't let her close enough to tear herself away. He would keep her at arm's length, at a barge pole's length. He would push her and Rory together, because they deserved each other; he would dance at their wedding and he would force her to remember whose wife she actually was.
And he would love her from afar.
He would admire her beauty, her passion, her kindness, her sarcasm, her confidence, her tenacity and her flaming hair, but he would do it as one would love a goddess. She was to be intangible to him. Something to worship, but never to reach. It was so comfortable, to love her in this fashion. Effortless and harmless; how could she hurt him if she never touched him?
It was the easiest option, the coward's option, but that was the Doctor: coward. Every time.