So, you put some odd symbolic interpretation on a perfectly normal act, and that makes it a crime worthy of death.
A more Biblical answer is that in those days God was prone to killing Israelites in large numbers and anyone who set him off had to be blamed for it.
The stoning is in Numbers 15. God kills Israelites in Numbers 12 and 16 and threatens to kill them all in Numbers 14 until Moses talks him out of it. (And I am aware of at least one more example in Numbers)