Posted: 20/05/2011 at 08:57
I think my answer to this would be
Neo's sub-domain of the Matrix (the only place where his powers are effective) exists within the Universe domain.
The Jedi's domain extends to the whole Universe, of which the Matrix is a sub-domain.
Assuming the Jedi is aware he exists within a sub-domain, then he will also be aware that his powers can extend *outside* that sub-domain, and therefore defeat Neo by killing him in the real world!