Tony had always thought that for Pepper to stop being in love with him would be the best thing that could happen to the both of them. If she didn't want him, that eliminated his inner struggle to keep himself away from the woman he wanted to marry. If she didn't want him, he wouldn't be hurting her anymore. She could move on with her life and he could, well, not move on... He'd die with fewer regrets when his bum heart finally did him in.
He had not realized how badly it would hurt when he lost her affection.