Feeling Impotent in the Face of Another Vaccine Reaction

I have been dreading my youngest son's entrance into middle school. This is not because it signals the end of his childhood and plants him firmly into the tween years. No, I have dreaded this moment because I feel my hands were forced to comply with a government mandate to have my child immunized despite blatant evidence that it is not in his favor.

Six years ago, we visited the doctor to get Sean's required kindergarten immunizations. I was horrified when he awoke a few days later almost unable to walk and sporting a grapefruit-sized red welt at the dTap shot site. It was hot to the touch and he had a fever. I posted about the worrying shot reaction and although it subsided in time, it left me quite hesitant to encounter a repeat performance.

Alas, despite attempting to convince our pediatrician that we wished to conscientiously opt out of the vaccines, we felt our hands were tied as they continued to insist that he had to have the shots in order to attend public school. So, I scheduled the appointment and surrendered to the inevitable.

He seemed fine during the shots, but woke a few days later with some swelling and redness:

I don't know if he would be exhibiting a high fever because every morning he clamored for a dose of ibuprofen for the pain. I guess what irks me the most is that I ran across an advertisement for the meningoccocal vaccine (the one he is experiencing an allergic reaction to now) that clearly states individuals who have exhibited an allergic reaction to a diptheria vaccine should not receive the meningoccocal vaccine. Yet, despite evidence in his medical files, the doctor urged us to put this agent into our son's body. (Side note: I doubt it was adequately documented when he spiked significantly high fevers after his infant shots - something I had forgotten entirely, until I pulled out my own medical records recently and reviewed them.)

I understand that meningitis is a serious disease. I have friends who lost their ten-year old daughter to spinal meningitis. I'm sure they would have preferred to endure this minimal allergic reaction, but I'm feeling quite frustrated that I'm being told he'll have to have an additional dose at age 16, and possibly again as a freshman in college. Who's to say the next allergic reaction won't be more significant? Who is monitoring the safety of vaccines? Moreover, why can't I, as a parent, decide what is in the best interests of my child?
===========
Recently came across this YouTube video that bears out some of my questions concerning the safety of these vaccines and perhaps the reason my doctor insists my child continue to receive, contrary to evidence of allergy (it all comes down to money, doesn't it?):