Logline
When Captain Burnham is trapped within a “mindscape” designed to test her worthiness to retrieve the Progenitor’s powerful technology, Book, Rayner, and the crew of the U.S.S. Discovery must hold off the Breen long enough for her to escape.
Written by: Lauren Wilkinson & Eric J. Robbins
Directed by: Emmanuel Osei-Kuffour
That’s a hell of a gamble if your objective is to protect civilians (and likely a gamble they would lose, considering the Breen’s actions).
I think the answer is the same - it’s not something you want to screw around with if you’re trying to save lives.
They faked the ship’s destruction, letting the Primarch think he could pursue the objective at his leisure. He could take his time being petty and destroying the Archive. Discovery visibly escaping would put him under time pressure. If he delays to indulge his pettiness, Discovery could get the technology. They’d be using themselves as bait to lure the Breen away from the civilians.
Also, the Primarch only made his threat against the Archive later. If they’d jumped immediately after the away team was aboard, it would have been before the threat was made. It also would have been before the Breen’s weapon demonstration, so the Archive would have been 100% intact when they left. At that moment, they had every reason to believe that the Archive was only in danger due to their presence. The logical, civilian-saving response would be to remove their presence.