This was an Ironblood Mother Ship, so naturally, there were no shortage of Ironblood Warriors on board, totaling around seven to eight hundred people. Fang Zheng could have killed them all if he chose to, but firstly, it would be a waste of time. Secondly, the risk was too high. Moreover, Fang Zheng had to worry whether they would manually self-detonate as they did on the Hunting Planet... Despite the size of a cosmic warship, just blowing up the engine or other vital systems would be enough to disintegrate a warship completely.
Fang Zheng didn't want to turn this expedition into a movie trilogy, so after he brought Nymph onto the mother ship and had her rewrite the operating system, he adopted a different approach. He sealed the entire control center and then — vented the atmosphere.