Vaccines are good and have saved countless lives, but some have stronger evidence behind them than others. Vaccination policy varies from country to country and over time, depending on the cost and risk vs benefit ratio. For example, in the UK, children used to be routinely vaccinated against tuberculosis, but it was stopped back in 2003, because there are so few cases of TB the cost and risk of adverse events of the vaccine didn't justify it.
Lack of genetic diversity, intensive monoculture are issues with plants, not just animals, but don't pose the same issues to human health, because plant pathogens can't jump to humans.
There's nothing wrong with raw milk, as long as the milk and cattle are routinely tested for nasty diseases such as TB and it's clearly labelled so the consumer knows what it is. Ideally it should have a lable warning "Not to be consumed by pregnant woman, unless cooked.". People should have the choice.
Where I live all eggs are unwashed. I get mine from a local farm shop. They keep for weeks in my kitchen cupboard. There's nothing wrong with washed eggs, but unwashed are more environmentally friendly, as less energy is required to process and store them.