Hi K.,
When I read your post, it sounded exactly what I went through 7 years ago. My son screamed and spit up when I gave him the Poly-Vi-Sol, and it got all over him and me and made a mess. And I felt horrible giving the vitamins to him. He would see the eyedropper come out and would start screaming. I even tried pumping milk and giving it to him mixed with breastmilk in the bottle - and he would refuse the bottle with the Poly-Vi-Sol in it! Which is so upsetting because a) he still didn't take his vitamins, and b) I had to throw out breastmilk that I worked hard to pump! So I just stopped doing it. And both my son and I felt lots better about everything!
My pediatrician recommended the vitamins to my other babies as well, and the only reason for it is that they were exclusively breastfed. And with my younger kids I didn't even try the vitamins, because of the bad experience with my son. And all three of my kids are fine (ages 7, 5, and 2).
I don't normally recommend ignoring a doctor's advice, but in this case, I do. Breastmilk is meant for babies, and is loaded with vitamins. If you're worried about vitamins, ask you doctor if you should take supplemental vitamins - they'll make it into your milk, and your baby won't even notice!
Hope this helps, follow your instincts, and good luck!