Even if all four thrones must be filled, the prophecy says nothing of Pevences, just Adam's bone. Any human would suffice.
The Witch makes first contact with Edmund. She needed to know where a human could have come from. Edmund tells her that there are two humans that know of the passage to Narnia. Him and Lucy.
If she kills Edmund that leaves one remaining human with knowledge of Narnia, who probably will be more insistent on returning to search for her brother. She needs to create two more witnesses to eliminate all witnesses.
The witch doesn't know they will fulfil themselves the prophecy and is probably more concerned about other humans coming and completing the prophecy than just four young children.