I see the purpose of the new rule, but have the implications of such a POWERFUL ability been considered?
In effect, it will be similar to Mass Cure Light Wounds in addition to damaging undead AND making them flee! So you take the old turn undead ability, and add a fifth level spell on it for curing and another say second level spell on it for damage. And you get that three times per day or more, as of first level! Turn undead would become the ultimate ability... Evil clerics would have a reason to be feared...
I'd suggest that the turn undead deals damage to undead and keeps them at bay, but not fleeing. Fleeing is a bummer anyway, you have to run through the corridors to reach the stupid fleeing undead, or wait until they fall on you in another inappropriate time. Rulewise, damage as per the actual alpha version, and on their turn the undead that failed their save need to remain at least 30 feet from the cleric (i.e. move away if they're closer), unless they get attacked by the cleric.
Then, the cleric could trade his turn attemps for cure spells, a bit like spontaneous casting is now. Perhaps cure one ally of an amount equal to the turn ability damage (or whatever, it doesn't matter), but not a mass cure!
Inversely for negative energy, you could mass heal undead (and perhaps control them), you could also keep them at bay; or trade one rebuke attempt to deal damage to one opponent as per an inflict wounds spell (touch attack, single opponent).
Sky