NB: some messages from the mission in question
"This is Victor 3. We've entered a slaughterhouse, command. Casualty rate in the thousands, Shivan bodies are among the dead. Proceeding now to dock seven"
"The Shivans boarded us! They killed everyone! I've got thirty-three survivors in deck seven. There's got to be more below."
"They took him away (Bosch), with Gibson and Sarno and about a dozen others"
Wjhat I'm wondering about, in particular, is did the crew of the Iceni expect the Shivans?
Also, the use of 'took' implies that the Shivans pretty much snatched Bosch as part of their attack, rather than him going along cordially. I think that Bosch was fooled into believing the Shivans were going to be 'friendly', and expected all his crew to be taken with him - so he set the Iceni to self destruct after his departure, destroying the evidence. Except the Shivans surprised him by attacking immediately - they were unawares of the self destruct, so they proceeded to kill all the crew of the Iceni.
Incidentally, the message about 'casualties in the thousands' indicates that the Shivans were in the Iceni for a while - simply because the Iceni was a big ship, and they had a lot of killing to do.
any way you look at it, though, FS2 throws up more questions than answers. It's good from a modding perspective, but still a bit of a pain in the arse.