Unlike most of the pervs who marvel at the sex scenes and find them to be central to the plot, I focus on Lee's character and how unhappy she is, self-harming and locked up in her dysfunctional family's world.
I think the story is very optimistic, despite Lee's unhappiness.
The film has a very unusual take on self-harming and S/M relationship: it does not condemn it or portrays Lee or her boss as sick fucks. They just very unhappy people, feeling they do not fit within the conventional society.
Secretary shows how a fucked up family can put one through an extreme pain, which is, essentially, the story of my life. But the film goes even further, showing that the people who cause other pain (Lee's dad) are broken people themselves.