The simple culling Evil Gods was actually an action of no significance.
That was because the Evil Gods were corpses in the first place: the perished spirits of civilizations and remains of worlds. They were automated weapons serving the Mastermind, tools that were fully autonomous—destroying them or blasting them into pieces simply would not help the Multiverse itself, and could even be considered adding to the piles of refuse.
To provide an analogy, destroying a 'probability which had already been sealed' would not have actually changed anything because they were already dead. Hence, whether they would be removed did not matter, because it was similar to how destroying a weapon would not stop a war from continuing—all it could ever achieve was akin to dropping iron slag into the mud, dyeing the land a scarlet red through rust and blood.
Killing an Evil God therefore served nothing.
That was why it had to be put to flames.
