Although Gideon again shows that he is not truly evil because all he really did is send Hook on a journey he could of easily killed him and didn’t.
Hook is no good to Gideon dead. Hostages are useful, martyrs are dangerous. Don’t take away everything your enemy has to lose; leave something by which she can be manipulated. At the very least, Emma will now be distracted and won’t be able to focus on fighting Gideon. Gideon might also need Hook for a later stage of the plan.