I don't think John Jones would be working for Lex or Darkseid. Why would Lex send in the martian manhunter to unexpose the kryptonians? Darkseid if they are staying somewhat true to the comics would just send his forces in and try to take earth for himself with his powers.
I think that Jones is working for a woman seeing as it was a red queenthat was sitting in the middle of the chess board at the end of the episode. Who that is I can't wait to find out.