Link made the correct decision in an instant. He had just escaped from Morpheus' murderous plan but was in no position to be relieved or to even worry about his injury. He swept his gaze across the hall and hollered, "Jacker, Anderson, resume the attack on the Elemental Puppet!"
Everyone had left their original post following his injury, but Link was clear that their greatest threat was still the Elemental Puppet. Jacques was nothing but a chess piece in Morpheus' elaborate plan.
After Link escaped the ambush, Jacques had outlived his usefulness. Morpheus, on the other hand, was a powerful Legendary Magician. Even if only a part of his power was present in the form of a puppet, he was still extremely dangerous if not dealt with in time. It would only take him a matter of seconds to do something unexpected.