You certainly have a very difficult situation because, soon, your life's role will be dictated by the courts.
You and your wife have come through some pretty horrific months, with your accident and your injuries, a premature birth and now the vaccinations. Your job loss at this time puts additional strain on an already difficult time.
Life is long and there are many turns on this path of Life; this is just a very particular moment. Your wife's hormones are no doubt totally scrambled; she has had to worry about her injured husband, her premature son (about whom she is probably over-the-top protective due to his early birth) and a much-reduced household income. She should be discussing all of this with you and not her parents. You, on the other hand, have your injuries and healing, no job and now your concern over your child's health. If the first shot causes problems, then you have something to work with on the topic; otherwise, it is the first of many such discussions. Seeing how your health improves through natural methods is the first step. As life goes on, your son is not your wife and he may have a natural interest in following your ways.
There will be many, many issues that come up over the years; this vaccination situation is just one of them. Learning how to resolve the issue is the key. First, you need to get healthy, your wife needs some more time to get back on her feet; the finances need to get in order. You need to express support for each other and the marriage. Things have simply escalated.
Approaching the 10th with a plan for resolution would seem paramount here. Marriage counselling? Maybe she needs some help to get her own system calmed down? Giving birth is one thing; prematurely, is quite another; her nerves are probably tattered (as yours) from this experience and she would be very leary of anything but the accepted protocol, particularly since this little baby was under the close eye of the doc since his birth.
Knowing what I know now, I probably would not have got our sons vaccinated, but they are fine; my husband and I are fine. You'll have plenty of opportunities to end your marriage -- you get lots of tests!! Marriage is a real challenge, but one worth tackling and winning. :) Almost everything can get resolved. However, there has to be an agreement from both parties to try to work out the difficulties. What is most important to you? What drew you to this woman in the first place? You need to recall this and hold it near your heart always.
Your son can survive by living with just his Mother, but he needs his Father every day as his role model. Your jobs as parents are to create a place of security and love so that this little person can grow to be a confident and self-sufficient adult who is able to leave your family home and move through his own world with great self-esteem and whatever other traits will make him a great addition to this world.
It is only when we are further down the Path of Life that we can look back and see the results of the various challenges that we have had, what we did about them and how the lessons learned all weave together into our own tapestry of living.
Since you have little time until Court, try visualizing the three of you together in happiness; send love to your wife and child and even to your in-laws. If nothing else, you will feel good about yourself and you may find pleasant resolution.
My very best wishes on the 10th; may things resolve as you would like.