TeenHealthFX is concerned that you may not have the best interest of your girlfriend at heart. Sex is not just an activity but rather an intimate action that can be shared between two people. It is important that you think about how this may feel for your girlfriend. You said that you were both still in high school, your girlfriend may not be ready to be having sex yet. As her partner and someone who cares about her, as you stated in your question, you need to be open to how she is feeling. The worst thing for this situation is to pressure her. If she knows that you are frustrated and impatient, her body will sense this during sex, making it even more difficult for her to feel comfortable.
It is good that she went to the doctor and was checked out. When she went to the doctor, did she explain that she was having pain during sex? If she did not, she should probably see the doctor again and let them know. Sometimes females can have a muscle tightening called Vaginismus that can make sexual activity extremely uncomfortable and painful. Also, if she is stressed out during sex, her muscles can tighten up causing insertion of the penis to be painful. So have her see her doctor again to discuss possible ways of overcoming this.
If she cannot talk to her doctor about this, have her call her local Planned Parenthood. If she lives in Northern New Jersey, please call the Adolescent/Young Adult Center For Health at (973) 889.6350. Both Planned Parenthood and Adolescent/Young Adult Center For Health can see teens confidentially and without her parent's permission for sexual health reasons. It is a good idea if you go to the doctor with her, so you can both discuss your concerns with a medical professional.
You had the right idea about taking it easy for a while. Maybe your girlfriend needs to become more comfortable with you and your relationship first. If it is truly the right time for the two of you to be engaging in sexual activity both you and your girlfriend will feel comfortable. The best advice that TeenHealthFX has is to be patient and accepting of how your girlfriend is feeling. Don't push and take the relationship slow.