If Charlotte & faraday told Jack & the crew they ran thr risk of being overtrown and using the threat of the gas against them unless they get answers and get everyone off the island and on to the boat. Thereforte they need to do it in secret first and explain after.
Ben knew the gas would be a major aspect of the plan of whitmore either from his source on the boat or because it's common sense that whoever controlled the gas would have control over the lives of everyone on the island and that means power.
So, i believe that when ben was being held at the end of season 3, he asked his Alex, Karl and rousseau to do him a favour. The favour would be to go to the Temple and get Harper to force Juliet to kill Faraday and Charlotte.
We already know he wants them dead, he shot Charlotte in the chest.
If he can kill the staff of the Freighter he can re-group and make arangements for the next wave of invasion and protect the Island from Whitmore and or Dharma.

QUESTION: I am thinking that the Tempest is quite important, it provides power to the island and holds a powerful gas that has the power to kill everyone. WHY WAS IT NOT GUARDED???????????????