I remember playing the retail version of the mission before the FSO version. In that iteration, you could stay as long as you liked blasting at the Dragons. In the FSO version, there's a time window open for your escape. This makes the warnings Command gives you more realistic, but changes obvious factors...
On the bright side, you might want to consider getting out pretty quick. If you try to jump out while being shot at, your ship will never slow to 40m/s, thus meaning you're going to die. As far as saving the Trinity goes, isn't it set to blow up after a period of time anyway?
-Thaeris