I disagree with everyone's answer thus far. It should be,
"before he had breakfast." (past simple)
Normally, the past perfect precedes the conjunction before and follows the conjunction after:
"I had run a mile before I ate breakfast."
"I ate breakfast after I had run a mile."
In the example given above, "He was killed before he had had breakfast" is incorrect English; it should read:
"He had been killed before he had breakfast."
The reason for this is that his death occurs prior to his eating breakfast. The past perfect is used to tell the listener or reader which event or events in the past occurred first:
"I had answered the question before the teacher asked it."
"The teacher asked the question after I had (already)
"I mowed the grass after I had eaten lunch.
"I had eaten lunch before I mowed the grass.
Now compare the last example above to the following sentence:
"I ate lunch after I had mown the grass."
In this example, my eating lunch follows in time in the past my mowing the grass. In the original example, the actions are flip-flopped.
I hope that might have helped you out. Take care and good luck.
P.S.. The examples given by others in which the past perfect follows the conjunction "before" and the past simple precedes the same conjunction is often heard in spoken English, but it is merely a common error in speech. In other words, it's incorrect English, but it's pretty prevalent. Like the subjunctive mood, this is another pet peeve of mine regarding how native speakers use the language.