There was a bond between them that nothing would ever break, not being kidnapped, nor being separated for centuries, and not even getting zapped back into the past. Amy and Rory belonged together; wherever her husband was, that was where Amy needed to be. How could the Doctor not understand that?
Rory would live to the grand old age of eighty-two, it said so right there on his gravestone, but he wouldn’t live that life on his own. If the Doctor wouldn’t help her get her husband back, well then, she’d just go and join him.
Nothing could be simpler.