Ideally the Hinton and the Iceni should arrive at the waypoint at sufficiently different times for this to work ok, but that doesn't seem to happen very often. Typically if you do a good enough job of protecting the science cruiser, it will keep pace with the Iceni (which slows down as it incurs damage to its engines from Vasudan attack) and will collide at the node. If you let a couple of asteroids get through and damage the Hinton's engines, or keep the Iceni's engines intact, the timing works out. The Iceni is among the fastest capital ships in the game so unless it loses an engine it should get there and jump in time to clear the Hinton's approach.
Though once I had the Hinton get there and sit in the Iceni's exit path as the Iceni jumped. I was forced to watch helplessly as the Hinton sped away at 200+ m/s. When the Hinton finally got its bearings on the navpoint again, it was 5km away and right in the middle of an active asteroid field. Needless to say, I was unable to save it and was therefore very ticked at its stupidity.