I actually gave the mission another few playthroughs yesterday...and in one of them, something rather odd happened.
So I killed the Ania and Thalassa (was that the name of the second Deimos?), all good. In the second half of the mission, I wasn't really paying attention and I ended up doing too much damage to the Diomedes, who jumped out and activated the bomb. The Yangtze then said it was scrambling to see if it could jump in time, Simak was calling me out, blah blah blah...and then the Yangtze reported that they wouldn't make it in time. I decided to stick around to see the blast, and the meson bomb blew up...like it was a normal cargo container. Nothing was even damaged. Then the Yangtze jumped into the gate, sent their heartfelt thanks, and...uh...nothing. I couldn't fire upon Simak, the Diomedes and its transports were gone, the bomb was dealt with, and the Yangtze had escaped. So I just tried jumping out then, to see what would happen.
I got the 'great job yaaaay' debrief music, but the actual debrief text was essentially a mission failed (due to Yangtze dying from the bomb blast or something). I was all kinds of confused.
Also: what's the deal with Simak station flying all over the place? That Arcadia was moving faster than a Kentauroi (by a factor of 2-3) and turning on a dime like it doesn't afraid of anything.