I may have found a variant of this bug. I just died 4 times in a row while placing turrets. After placing something, I essentially self-destructed with the kill message "killed by collision with Falcata 1." After reading around the forums for a bit, it occurs to me that this might have happened after deploying an ECM pod each time, but I'd have to go back and test again to be sure.
I've played through this mission a few times with no incident (other than the repair pod seemingly doing nothing), and the only thing that's changed between then and now is I updated to the 3.7.1 BP build.
edit:
derp. i WAS getting flung to the far reaches of jupiter. dying like that is what happens when you reach the edge of the mission space. i didn't notice because it was happening while i had the map view still up. and turns out, not necessarily tied to ECM pods. i finally managed to make it through, but got two more instances. one was the same as all the others, happening as i set turrets at the start, the other well into the mission after i added a turret later on. the first one happened after placing a flak, the second i don't remember. but i do remember that this one was delayed. i was out of the map mode and back into the flying for a few seconds before it happened. the time i made it all the way through, i didn't deploy any ECM or the repair, but did deploy all the weapons eventually. i did it slower, coming back out of map mode every one or two deploys. maybe it's tied to how fast you deploy things? would a debug log be of assistance?