This quote is an example of anaphora. The word “it” is used to refer to “knowing.”
Anaphora is a stylistic device used to emphasize. In this case, the emphasis is on “knowing” that there are other people like them. They have been rescued.
'Knowing makes all the difference. Knowing that we're not just pointless freaks -- a few bewildered deviations hoping to save their own skins. It's the difference between just trying to keep alive, and having something to live for.' (ch 17)
In this case, “knowing” is repeated twice, and by using “it’s” the third time, the emphasis is on the effect of the knowing, rather than the knowing itself.
David and Rosalind are free, because the Sealand people have come to rescue them. They are no longer ostracized and victimized for being telepathic. They are free, and going to a society that appreciates them.