> the body as a whole is not something we can predict the longterm effects for

I'm no doctor but I feel like modern medicine can make some pretty darn good predictions.

Besides, your arguments are not sound. If your premise of "the body is too complex to predict" is true, then you can't immediately follow that with a prediction of a long term effect (e.g. eliminating a "harmless" disease will have ill effects.)

I can just as easily make something up like, "the immune system can only respond to a finite amount of disease, therefore getting vaccinated leaves more capacity for future infections." (which is not true)