What is the difference between overriding or destroying the Control Towers?

Both overriding and destroying a control tower will disable the machine and choosing either option will award you a trophy after disabling them all.

Whether you choose to override or destroy, the key difference to keep in mind is that overriding the control tower will send out a shock wave that will stun all other machines that was under it's control for a short period of time.

Choosing to override the control towers is particularly useful