What happens to Infiltrating Cylons on New Caprica when Galactica jumps away?
Pegasus rulebook, pg 7:


  A Cylon Leader is considered a “human
  player” when he is Infiltrating and a
  “Cylon player” when he is not
  Infiltrating.


I don't see an exception for infiltrating cylons on pg 17:


  Once the Admiral has ordered Galactica
  to leave and ended the game, destroy
  all civilian ships still on New
  Caprica, and execute any human players
  still on a New Caprica location. If
  after resolving those losses, no
  resource has been reduced to 0 or
  lower, the humans win the game!


Therefore, infiltrating cylons are humans and would be executed.