Thinking on it, I can KIND of understand the logic behind Venat's decision, if we assume our going to the past didn't originally happen. She may have been looking at it through the lens of their civilization, that they were shepherds of the planet, and the planet's needs came first. It gave the new life souls, so it wanted that life to live. The Convocation was willing to throw that life away, ignoring their sworn duty, and depending on how long she had tried to reason with them before, she may have come to the conclusion that they threw away the very goal their civilization had. So she performed the last deed that followed that mindset...she Sundered all life and Zodiark to seal him away and safeguard the planet. No more would any dictate the planet's will, the planet itself would decide what it wanted, and life would flourish as needed.
She may have tried to lessen the mental load of it with the thoughts that it was essentially going to be
fission, dividing the one into many that will ultimately resemble the original.