Let's discuss the differences between several possible alternatives, starting with:
John, who was in a blind fit of rage when he found out that the organization had killed his parents...
- saw them dead in his mind
That's a bit awkward for what you're trying to say. Consider an example with the opposite - "John's mother was overjoyed to see him alive after coming back from war." What you probably want to say here is "imagined the sight of them dead", or "had a vision of them being dead". Consider also this example: "Steve's mother would always worry whenever he jumped on his motorcycle. No matter how hard she tried to repel bad thoughts, she always saw him dead in a ditch somewhere." Given that John's parents have already been killed and he knows it, the situation is no longer hypothetical like in that example, which is why the sentence sounds odd to me.
That's talking about a witnessed event in the past, and would imply that John actually saw his dead parents in real life, and didn't just imagine the sight of it.