As you guys pointed out, the law is not perfect in this case.
A herper gently handling a snake might get caught and fined, while a person killing a snake in his backyard will not.
This is due to several reasons:
1. There are no rangers hanging out in people's back yards (that would be kind of creepy), so there is no one to catch you.
2. A person killing a snake in his back yard is doing it out of ignorance and (un-justified) fear for his and his family lives.
3. The wild (state "owned") is not a back yard (private property)
4. A herper is actively and knowingly going out to the wild to search for protected wild-life, he knows what he is doing.
5. A person killing a snake in his backyard is "dragged into" a situation he did not ask to be in.
I invest A LOT of energy in educating people in Israel about the benefits of having snakes around, how to identify the dangerous ones and the legal status of all vertebrates in Israel (all are protected aside from pests), but enforcement resources are limited and the legal departments are not keen on prosecuting ignorant people who felt they were acting in self-defence inside their private property.
As I said, its not perfect, but I rather have some law than none at all like some of our neighboring countries were traders run amok and destroy whole populations of endangered animals for pure greed.