In factions.rul
Jack sparrow:
Cntrl-f AuroraGamesStart and AuroraGames, change both executionOdds to 0.
late game: technocracyFirstStrike and technocracyStrike change both executionOdds to 0.
Alternatively, to allow shooting them down, change STR_VESSEL_MISSILES_1 anf STR_VESSEL_MISSILES_3 (lower speedMax probably)