bible allow religious killing worse than islam, page-12

therefore, how is this commandment: "Thou shall not kill/murder" to be interpreted?

It could be interpreted as killing is a sin against God.
Mitigating factors could be if not killing was also a sin under the circumstances. Moses had a choice, kill 3000 or have most of his people at risk of becoming Godless and facing death. He chose the lessor of the two evils.