We know Halcyon and Knight are dead from the "Good Losing Ending" of Wing Commander II, I.E., the one where you don't destroy K'Mang but instead blow up two Fralthras in Gwynedd. The conversation that plays when you shoot down Jazz in this ending is different from the one in the K'Tithrak Mang ending.
This is also raises some questions on who communicated with whom. Because Freedom Flight was written before Wing Commander II, and Hunter was alive in the novel. However, this quote seems to imply that he died on the Tiger's Claw. And apparently, the producers of Prophecy forgot this line when they brought up Iceman as well.