That ending doesn't change Maul's death or survival. It was originally intended to be inserted if the death used resulted in a PG-13 ending, but it wasn't necessary. It still leaked out in some 35mm prints.
If that was the ending used in 1999 (because the bisection resulted in a PG-13 rating), people would still think Maul died, and he would still be dead for the past twelve years (unless the EU resurrected him).
If Lucas made that change on the 2004 DVD release, people would still think Maul died, and that Lucas was just toning down the violence.
That ending does nothing to change Maul's death. TCW changed Maul's death. So I don't see how the change would be any different than putting Ian McDiarmid into The Empire Strikes Back, or dubbing Temuera Morrison for Boba Fett. It's just making The Phantom Menace more consistent with a later story.
So the question is whether it's acceptable to alter a film to better fit the story at all? Or if it's pointless for fans to pick and choose which alterations we like and dislike, whether it's Ian McDiarmid in Empire, Temuera Morrison in Empire, Hayden Christensen in Jedi, or, potentially, Darth Maul's more survivable "death" in Phantom Menace?
I don't doubt that many of the people that are fine with Ian McDiarmid in Empire are also opposed to Hayden Christensen in Jedi, for instance. I'm definitely not a fan of replacing Jason Wingreen with Temuera Morrison. But unfortunately, the final arbiter on the changes is George Lucas, not any particular fan, nor are we going to find cuts of the films that satisfy all fans -- except, potentially, their original theatrical cuts. But that takes us back to whether it's acceptable to alter the films for continuity purposes.
"Trust not the words of a poet, as he is born to seduce. Yet for poetry to seize the heart, it must ring with the chimes of truth.”
“The world is understood through metaphors. Language is a metaphor-system. Mathematics is a metaphor-system. All real-world schools of magic and religion revolve around the understanding of vast metaphor-systems, symbols as they relate to concepts."
"See, the thing is, everything everyone tells you is a lie. The truth is always bigger than the words we use to describe it."