The Yellow Emperor's cultivation isn't as advanced as Emperor Jun's, and similarly, Emperor Jun wouldn't go as far as to kill the Yellow Emperor. Both are resurrected by Nuwa, and their main purpose now is to help Nuwa reshape the order of the living realm. As for killing Ye Fan, it's just one of the means to reshape the order. The Yellow Emperor can't wait to kill Ye Fan so that Ye Fan's soul would dissipate forever, whereas Emperor Jun thinks there's no need to fuss over Ye Fan. The two have different philosophies.
"Lady Nuwa has already completed her task; I don't need to explain anything to you. If you return to Lady Nuwa, I'd actually consider you a somewhat intelligent cultivator. But if you don't return, haha, you'll die without even knowing how!" Emperor Jun gave his final warning.
