I actually agree that all evidence seems to point that he is the core part of the Iifa tree stopping the sorting of souls. Thats why when Kuja kills you appear before Necron, because the transfer of souls has been stopped by Necron. It also does explain why the Iifa tree dies, you can't live without your heart right? It would also explain the moans in the background of the Hill of Dispair, those are other souls that haven't returned to Gaia.

Look at their theories of pain, life and death.

Garland
(In Pandemonium on Terra.)
"But think for a moment... Isn't life death itself? It must kill other
life-forms to survive..."
"Sometimes it even kills those with whom is shares blood..."
"To live is to give life meaning, yet one must take others' lives to
survive..."
"A mature civilization becomes aware of this paradox..."
"Terra's souls will sleep until they forget such nonsense. They will begin a new life in a new dimension."
"It's a world in which life and death become one..."
"That is the dimension in which we are meant to live, as beings that
transcend life and death!"


Necron:

(Above the Hill of Despair.)
"All life bears death from birth."
"Life fears death, but lives only to die."
"It starts with anxiety."
"Anxiety becomes fear."
"Fear leads to anger... anger leads to hate... hate leads to suffering..."
"The only cure for this fear is total destruction."

"...Now, the theory is undeniable."
"Kuja's action proves it. All things live to perish."
"At last, life has uncovered this truth. Now, it is time to end this world."

...

"I exist for one purpose..."
"To return everything back to the zero world, where there is no life and no crystal to give life."- That line also proves Kuja didn't destroy the crystal, that was Necron's job.
"In a world of nothing, fear does not exist. This is the world that all life
desires."


But here if you need some more facts to look at...
http://db.gamefaqs.com/console/psx/f...sy_ix_plot.txt