To the Zerg, an empress was equivalent to the commander of an army.
Moreover, this ability was far above a commander-in-chief. If humans were to send out equal forces to carry out army-level operations, the Zerg Empress would definitely win.
This was because its micro-manipulation ability was extremely precise, and the Zerg coordinated extremely well, better than any strictly-trained army.
Therefore, the best strategy against them was to 'behead' this brain!
An army would become a bunch of lost bugs once they lost their brilliant commander-in-chief. The consequences were even more severe with the Zerg.
Therefore, the Human Alliance dealt with the Zerg by seeking out the empresses at all costs and sending their elite mechas to behead them!
What Fang Yuan did was more excessive.
The Undead Immortals and Grand Arcanists had to attack the flesh nests forcibly once they found the entrance.