Okay - First, good job on standing up for yourself!
Second - Try to cut the doctor some slack.
Doctors/med students are assertive by nature, and one of their biggest frustrations in life is running into people who have no medical training telling doctors "what is what" in the medical field. Especially if the information came off the internet because so very, very, very much information on the internet is wrong. Doctors take the view that you have no idea what you are talking about. For a short period of time in my life I was a medical grant writer. It was amazing how quickly their tone changed with me when they found that out. Suddenly I was "more educated" than I was 3 seconds before they knew that. *Rolls eyes*.
As to the student coming in. In a teaching facility, it is very common for the med students and residents to follow the doctors like shadows. Some of this is to educate the student, some of this is actually for the doctor's protection. Ears that hear and eyes that see can prevent law suits later down the road. If you are uncomfortable with a medical student or resident in the room you should speak up and say something. Do not, though, be surprised if a nurse replaces the med student.
Next time you want to debate the vaccines, do NOT come to the doctor with, "I heard," or "I read." Come with the article and source in hand.
In your eyes, you are preventing your child from receiving fetal tissue.
In that doctor's eyes, you are possibly exposing your child to a deadly illness, and in turn, exposing others to a deadly illness.
You just have to show him that you are not some fly-by-night person who picked up information at some cult-meeting, and rather that your source is a reliable, scientific report.