I am on the pill and I have protein s dificiency it is a pegesterone only birth control
I was diagnosed with Protein S Deficiency, too, and was told not only could I not take the Pill, but any other contraceptive that deals with hormones or I could potentially die. Very upsetting. Was diagnosed after a miscarriage. Pregnancy can put you at higher risk for danger and I am only allowed to use condoms and spermicide. That's it.
This section discusses birth control and thrombophilia specifically.
http://www.fvleiden.org/ask/23.html
Towards the mid-to lower portion of this article, the doctor discusses Protein S deficiency and other issues in detail (the first part is about other blood clotting disorders). He does not go into birth control options, however.
A hematologist would be the best person to advise you as to your birth control options and impact on your clotting disorder.
http://www.fvleiden.org/ask/50.html
I have a factor II prothrombin mutation and have been told that I can fairly safely take a progesterone-only-pill (POP). I was told that even safer than this would be the Mirena IUD. Search for Dr. Stephen Moll's page on blood clots... he has a nice chart describing the relative risks of birth controls for people prone to blood clots.
I do not know for sure if Protein S deficiencies pose different problems from Factor II ones... (I actually had a pulmonary embolism last year and consequently stopped taking the combination pill), so please be sure to check before you decide to do anything, but it seems like these might also be options for you. I think I remember that no positive link has been identified between the POPs and blood clots.