I've been thinking of this off and on all day, trying to formulate a response.
First of all, the health department is not at all at fault, AT ALL. Never has it been required for both parents to agree to anything medical. In most families, it is the stay at home mother that handles all things medical. Think about it, has the ped ever asked any of you if the father agreed to anything? Nope. What about the OB? Does the OB ask the father's opinion before administering an epidural? Nope.
Also, the health department was giving the child the normal vaccines at his age. It's a lot, and if he had been vaxed on schedule up to now, there would have been less (or they could have been spaced out a bit more).
As for the husband doing it behind OP's back...I don't know. I'm very torn on this. How many times do we as mothers do things that our husbands don't approve of? Or do we just not tell them about? Heck, I know a woman who breastfed her 2 year old "in the closet" because her husband disapproved of it past age 1. I know you guys will say that there's no comparison, as vaccines are at least potentially dangerous and breastfeeding is not. But the father in that case did think it was "wrong" to breastfeed. Is his opinion somehow less than the mother's? Often the stay at home moms make decisions for the whole family, including the family diet (since she does most of the shopping), the family schedule (since she is the one home to enforce it), rules about tv, rules about friends, decisions about schooling, etc. Now, I'd hope that in most cases, those decisions are at least somewhat a family decision, and the husband has some say in it, but most often the husband just takes a 'whatever you want, honey' stance.
Now in this case, with the OP specifically saying NO, and the husband doing it anyway, THAT speaks volumes for the state of the marriage. There evidently are little to no communication lines open, little to no respect for each other's opinions, and that goes BOTH WAYS. The husband had a true concern that he felt wasn't being addressed. Whether that is true or not doesn't matter, only that he felt he was being ignored, and had his son's well being at heart. I would be IRATE if I had a concern about my children that my husband wasn't listening to, and then yes, I would take matters into my own hands if necessary. In fact, I have done just that. I was very concerned with issues my middle son was having as an infant, and kept taking him to specialist after specialist. My husband, probably in denial, said I was making it all up. For a while I stopped taking our son to drs, then I couldnt' stand it anymore and I started scheduling new appts for him. I didn't tell my husband, I didn't go out of my way to hide it, but I wasn't exactly forthcoming either. Once the drs started uncovering problems, I started talking to my husband about it more. But I guess you could say that I did go behind his back to get my son medical treatment I thought he needed. It was a division in our marriage for a time, the whole situation was very stressful, having a baby sick with something unknown. Eventually we got a diagnosis, and after that stress was removed, we were able to work on reconnecting as a married couple and we now have a strong marriage.
NOW...that said. I am the product of divorce. Several divorces, in fact. Two of them ugly, including long drawn out custody battles, counseling, court-appointed psychological testing, etc etc etc. I will be the first to tell you that it's not ideal, but I'll also point out that I am a successful college-educated adult, in a very well-paying career, in a happy marriage, and am a happy person. DESPITE coming from a horribly "broken home". Divorce is not the evil it's made out to be. It does not have to equal horrible childhood or unsuccessful adult.
Also, you do not lose all rights to decisions if you divorce. In fact, the decision making for things like medical care can be written into the divorce settlement and custody arrangement, and if a parent goes against it, then that parent risks losing visitation. Decisions may become more complicated, but let's face it...they're complicated right now! You have no idea what else, if anything, your husband has done or will do.
If you and your husband can't come to an agreement on how you're going to make parenting decisions, then I think there are serious issues. If this is a chronic issue of him not respecting you as an individual, then there are already serious issues. I have too much self-respect to allow someone to disrespect me, if that makes any sense.
OP...I have no idea what I'd do in your shoes. I think I would first make sure that your son is okay, then I'd have MIL keep him while you and your husband take a LONG time to talk about a LOT of things. Not just this one issue, but EVERYTHING in your marriage that has ever been contentious. You can't go into this discussion thinking that you are right, though, you both have to go into this willing to openly listen to the other person and truly consider their thoughts, feelings, and desires.
Good luck. This is going to be a long process if you want to trust him again.