My guess: The reason Manabu cannot stop Yukari's death is because she herself is the irregularity caused because of her approaching of Yukari in the first place. The Nanami in the beginning that tells her to, "stay away from Yukari/you don't understand anything", -is- Manabu. If she doesn't get close to Yukari, she's never hurt, never "repaired", and Yukari is no longer the cause of creating the irregularity Manabu becomes, and there is no need for Yukari to die.
One could argue that Manabu disproves this by completely altering the past, yet still having the "cell phone", but she is still tied to Yukari. Calling it "fate" or "destiny" sounds lame, but think of those as the universe's "paradox prevention/correction systems". The two of them cannot exist "together". Manabu has to decide the path herself to not become involved with Yukari, only then will Yukari not have to die. And then "Super Kami Gaku" wont happen, and everything will be at peace. (Unless the Alice that was "saved" during Mahou Shoujo time ends up breaking reality somehow. You saw those eyes. Never leave loose ends.)
Just my speculation. It probably wont end so "simply", instead having the universe blow up, or reality unwind, or something.
