Joe Ga had originally harbored no hopes of capturing any important figures...
His sole intent was to annihilate everyone in the warehouse and then present their corpses to the CIA as a grim token.
However, since Frester, who seemed to be the leader inside the warehouse, had survived until the final round of shooting, Joe Ga obviously couldn't just kill him off simply.
Joe Ga was well aware of what the big shots behind Eric wanted, and this living witness was valuable.
Sanderson ultimately couldn't bring himself to shoot the panicked young technicians, who were clearly logistical staff and didn't even have weapons.
Joe Ga could understand Sanderson's adherence to honor, so he simply had these young ones help pack up the bodies and then knocked them out before they all retreated together.
The idea of having the Shadow Messenger act to coerce a confession out of Frester came to Joe Ga after meeting with FBI Director Cooper, who had come to provide assistance.