If he had wanted to kill us, he would have done it at the junkyard.
If he wanted to kill us, he would have done it at the ju kyard.
Both the sentences are grammatical but different in meaning
The first sentence is conditional type 3. It indicates the past condition with the past result. He didn't want to kill us, so he didn't do it.
The second sentence is a mixed conditional (type 2 + type 3). It shows the present condition with the past result. He doesn't want to kill us, so he didn't do it.
Another example of this type:
If you needed my help, you would have asked me