The flaw in your logic is subtle, but huge.
They said in plain english that they were going to detonate the energon, and that would rip the planet to atoms. Megatron said it himself, and he isn't exactly stupid.
Remember, the planet was riddled with energon, detonating a chunk of it could set off the rest.
Of course, the huge kink in the Vok's plan is that annihlating the planet would take out the matrix, and them in the process. They would still exist, but as the swarm.
I think, anyway.
The Logic of the Vok (or lack thereof)
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