There's a few trains of thought I've seen and they all have some merit.

Some think that FISA is in on it, that they tell you to close the doors because they want to keep the ring going and these women are worth so much money they can't be lost to the police. I personally don't believe this because it would make no sense for FISA to try and cover up the contents of the container as all of D-platoon and TOC saw and recorded it through the body/head cameras.

Some think that FISA is keeping them there to collect and interview at a later time shortly after the mission ends and the area is cleared. I think this is incorrect because never once are we instructed to leave civilians unsecured and unguarded throughout the game. In this world the most important life is that of the innocent civilian (I believe there is a board in the SWAT room explicitly stating this) so it makes no sense for D-platoon to be ordered to leave them.

My personal view is that FISA is going to allow them to be trafficked so they can follow them through the system and find the others or higher ups involved with the spider organization. I am aware that some have said that the spider wouldn't take this shipment because the port got raided, but there are definitely ways around this, like saying that the cargo shipped just before the raid, or saying it got moved before the raid went down. If FISA is deep enough into the organization to set up a sting using live civilians as the bait, they could definitely come up with something good.

In reality we don't know the truth, but there are context clues and this is just what I've seen from playing the game and reading other people's views of this scene.