Think of the resources that the Sphere Builders would have had to invest into invading normal space. The destruction of the Spheres meant the loss of all of those resources. Destroying the Spheres could have been all that was needed to stop the threat. The Spheres were the Sphere Builders' entire ability to interact with normal space. They may not have been able to go back without the Spheres in place.
Those resources invested in the Spheres could have been way too finite, in Sphere Builder space, and completely invested in the invasion attempt. After the Spheres were gone, the Sphere Builders would be completely cut off from those resources, and physically unable to stage another invasion attempt, even a small enough incursion to prevent the Spheres' destruction.
Another possibility is even simpler: The loss of those resources could have crashed the Sphere Builders' economy, and led to a change in Sphere Builder leadership to those less likely to pursue an invasion of normal space, and there was no will among the new leadership to fund another incursion to prevent the Spheres' destruction.