Volition
Pepper knows that she's the only in the crowd that really had a choice.
Tony was born into such a family with his talents and he was expected to be something all his live. Thor – the same, only a bit different. Bruce's research proved unfortunate and forced him to do a lot of things he wouldn't have done otherwise. Clint and Natasha, parentless childhood and necessity of finding their paths. The closest to having a choice was Steve because he was asked if he agreed to the program, but given his life story he could never refuse.
Pepper comes from a normal family. She has parents, happily married, a sister, and numerous relatives. She chooses her major and minor according to her own wishes. She chooses her first work since she's smart and has a variety of possibilities. She chooses to agree to be Tony's PA because she wants, because he intrigues her. She chooses to be his girl and then chooses to end it and there is no compulsion whatsoever. The bonds just dissolves slowly and painlessly.
She chooses to stay and she will always choose to stay because there is nowhere she'd like to be more than here.