If Magus Xion had indeed firmed up on his decision, with the power that the man had, he could take off with the crystalized stone and no one on Earth, even Emery himself, would be able to stop him. Even so, the man still let Emery be the one who decided what to do with the stone.
Emery knew that even if he chose to give the stone following Magus Xion's plan to keep him from harm's way, there was actually no guarantee that Grand Magus Zenoia won't seek Khaos on Earth, or worse, harm him as soon as he arrived in the academy.
But even though the outcome for him was very uncertain, Emery agreed to follow his master's plan anyway.
The main reason he accepted the plan was actually not because he was afraid of the future. He was more worried that his master would be in trouble if he returned empty handed.
Therefore he let Magus Xion take the stone with him, somewhat accomplishing what Grand Magus Zenoia task him to do.
