"I know that the being before me has no soul. You are dead, John"
You didn't account for the Ship of Thesus Paradox in your calculations, though.
Replacing all the parts gradually would transfer his soul to the new, now pseudohuman homunculus that you still have the audacity to call "John."
Is it the original John? No, but due to the nature of cellular replacement and personality drift, he wouldn't have been the man you knew ten years ago anyways.
In fact, I'd argue that, since you (and, presumably, everyone else) still recognize him as the man he once was, you haven't destroyed him or his soul at all; rather, you have freed the essence of John from the frailty of human containment.

So good job! In your anger you gifted John with immortality!
From petty spite, you've birthed a transhuman ideal.