Thanatos knows of the evacuation function on the SCA. Lightning and Persephone used it right in front of him last mission. However, that isn't an option here.

"We risk escalating the situation. There is no guarantee that will break the illusion, and we'll be sending compromised people to unsuspecting passengers."

Not everyone leaves on the mission, and with such reduced numbers and skills, those who stayed on the train won't have the resources to deal with a sudden influx of people. There's no way to contact them either. They could send VoidTreckers back before them, but there is still a shortage of help. For both sides.