When civies are destroyed are they permanently removed like vipers or are they mixed back into the pile of random ships?

p. 22: The current player chooses a civilian ship in the area and flips it over. The resources listed on its face are lost, and the token is removed from the game.

Background: All population resources on the civilian ships added up plus the one damage token for Galactica equals the starting amount of population in an unaltered game. You cannot regain population - once the people are gone, they are gone.

If you would put the tokens back into the pile, you would effectively have unlimited population from which you can happily continue to kill.

You mean "unlimited potential for population losses". The amount of the population you start with is all you get, so you cannot "infinitely kill them".

It would just be easier to lose "the same" population again, since most of the ships are population-losers.