So... Kill it with Nuclear Fire before it lays eggs?

Honestly, if the plan was indeed to seize control, and use Synth's to improve lives, or even assert control and deal with Raiders but it's not. It's to use the Commonwealth as a breeding farm for test subjects, and bury their heads further and further in the sand.

And the only reason FEV was shut down is because Virgil destroyed the place. His notes clearly have him explain they were continuing long past the point they'd learned it was a dead end.