Oh, I would be so mad at my OB also. You should have gotten a new doc. I'm so sorry. Have you considered seeing a midwife? They tend to be more naturally minded. Doctors will always say that there is no connection between vaccines and reactions. They just don't. Here's a story for you: http://iansvoice.org/default.aspx
This child died after receiving the Hep B vaccine in the hospital. Every doctor/specialist insisted that the reactions he was having could not be related to the vaccine. They just wouldn't or couldn't believe that there could be any connection. In the end, it was determined that the vaccine was the culprit by the medical community. It was too late. The doctor actually did report it to VAERS (Vaccine Adverse Event Reporting System). Only about 10%-at most- are reported! So, the numbers of events that the doctors/pharma has are very skewed. Most doctors refuse to report because they don't believe it could be true. It is a crazy, vicious cycle.
The other thing about taking the flu shot in pregnancy is that you have now introduced mercury to your developing baby's system. It is a dangerous combination. This is also why I don't do rhogam shots. They contain mercury. Well, you can get non-mercury ones, which I do take postpartum if necessary (if the baby is +, and there is risk of blood mixing, which is not normal).
So, what can you do now? Fire your doctor. Get one who believes like you do. You should not be forced to get care that you do not want. You are hiring the doctor, not the other way around. That is bullying. Also, read the book, The Thinking Woman's Guide to a Better Birth, by Henci Goer. It will empower you. Take some essential oils. Get Young Living's Thieves Oil and diffuse it. You can also put some on your neck and throat, and on the bottom of your sock-encased feet. Take Vitamin D. Go see a chiropractor, who should be able to help you and offer more advice about healthy alternatives to pharmaceuticals, which are so not good for you or baby. And, the chiro might be able to offer advice on the mercury exposure for your baby. You probably can't do anything about that until after baby is born though because chelation and such is dangerous during pregnancy-I think. But, the chiro and a midwife should be able to advise you on diet and how to maintain the healthiest pregnancy possible.
Again, I am so sorry, and I would be furious. I know many people say that they get the shot, yada yada yada, no effects. Well, they don't really know. Does the child have ADD/ADHD, asthma, allergies, etc? They might now know for years, and even then will probably never make the connection. Look at the increase in these childhood diseases and I ask why. We poison our bodies and then expect health.
Blessings to you. I pray that you find excellent health care. Fire that doctor. Seriously!!