On the contrary in Derelict, a similar mission has a large enemy ship jumping in and causing the allied ship to reduce to health critical, so it tries to jump out. Several times in a row it gets neutralised as it's jumping out. I thought this was normal but the mission stagnated and nothing more happened - unpassable - for 4 times in a row! I finally try it one last time, amazingly the ship *finally* manages to escape and what do you know, return to base pilots!!!
Also I've had the Phoenicia destroyed many times because the inv probably got bypassed due to too much incoming damage and it goes from 5% to 0% in one "hit" somehow as the 4 BF Reds rip through it.
As for how the Phoenicia is in front of the juggernaught, it either has jump drives that recharge reaaally fast or the Sathanas didn't bother shooting until the ship was getting close...and you'd think command would know better than to stick something in front of the Sath after a corvette got vapourised in 5 secs. (Then again, it's command, YOU HAVE YOUR ORDERS!!!)