While following ion-trail of pirates, Enterprise encountered the sphere after crossing the cloaking barrier of sphere. Archer ordered to put Enterprise in orbit of sphere to find what pirates were doing there for 8 hours.
The main plan of trans-dimensional beings (sphere builders) was to eliminate humans. And, when Enterprise was put into orbit of 1st sphere, they got the chance.
As Enterprise was in Delphic Expanse at that time, it was easy for them to suspect that humans might screw their plans up. So, it was logical action for them to demolish Enterprise.
As Enterprise was very close to sphere, there wouldn't be any chance for them to survive if huge disturbance were produced (like that time near sphere 41).