Look at it this way: Falz Elder and his cousins were immensely powerful beings on their own, and they can't be physically killed. PD is their combined might, and even she was only a fraction of Xion's power, being a failed experiment. Xion can't be killed either, she chooses to be divided the way she does so nothing else can try to equal her. Luckily for all of us she was never into being destructive. Her weapons were meant as a means of self defense, but she admittedly poured too much of her conscience into Clarisssa.
If Xion chose, she could devote any amount of herself to Clarisssa, and she wouldn't need Matoi to do it. Imho Sega made Xion a little too OP.
At any time Xion could technically intervene and wipe out PD and everything she created, completely destroying even the time loop. But we wouldn't have much of a story mode if she did. That and she doesn't like getting involved.