If you do many missions after the crew gets abducted, time goes by and some of your crew will die.
From what I read, the earlier you go to the Collector's base after the abduction, the likelier it is the crew will survive. --- Currently playing: Left 4 dead 2, Darksiders, Torchlight Waiting on: Arc Rise Fantasia (Wii), Mass Effect 2 (PC), The Old Republic (PC), God of War 3 (PS3)
It's not just missions, it's time as well. I'd got all crew loyalty done before the crew got kidnapped, but I went off to do some mineral scanning to research some final upgrades before going through, scanned 2 systems worth of planets etc, and got the 'half the crew liquidated' thing. Not a single mission, just scanning about 8 planets.
--- Where's the Kaboom? There was supposed to be an Earth-shattering Kaboom!