We dealt with this issue with the last 3 children. My midwife didn't want to influence us either way, but I felt she was kind of reserved on the issue (against it). I had a hospital birth with a midwife with baby #5 in 2004. We didn't do the vitamin K with the last 3 children. Babies #6 (Eden) and #7 (Joshua) were c-sections. This article states that the risk of brain bleeding due to lack of vitamin K is 5 out of 100,000. That's .00005 percent!
This ointment is routinely applied to newborns to prevent complications due to std's--specifically chlamydia, syphilis and gonorrhea. The concern is a bacterial infection of the eye that may lead to blindness. Most likely, you don't have any of these std's, so this is not an issue for you. I will say this, I have Group B Strep during my pregnancies, so we did decide to do the ointment for my 5th baby who was born naturally, BUT we delayed for a bit so he could bond with me. If I had to do it over again, I would refuse it. My 2 C-section babies did not have it.
Here is an article regarding the eye ointment.
Our hospital was willing to work with us and our midwife and my OB have been very supportive of our right to choose. However, if I were dealing with a different situation, I would draw up papers stating my objection to the vitamin K shot, prophylactic eye drops, etc. and have them notarized. It would show them you are serious when you show up with that paper. Your husband should go with the baby if he/she is removed from your room after birth for any reason to make sure the medical staff upholds your wishes. Also, discuss your desires with your pediatrician before the birth.