You are confused. The bonus from giant growth does not yet exist at the time your thaumaturgist ability resolves (since the giant growth has not yet resolved). Therefore the creature dies.
Layering does not interact with the stack at all; the stack if for spells and effects currently being played to determine in what order their effects happen. Layers determine how different type of effects combine.
To put it another way: The stack resolves effects one at a time so that they can change the current state. Layering tells you what the current state it when multiple effects have changed it in conflicting ways.
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