Not so much actually. Will saves work fine.
If you run the numbers, and assume the cleric is putting some of his gear (just a small fraction) into increasing Cha, then a cleric has about a 45% chance of turning an equal CR undead.
Hmm.. looks like you're right. I wish I hadn't deleted the work I did the first time, in Excel. I went and made a new one - I started with a cleric with Cha 14, added the +2 synergy bonus, and increased his check by +1 every 5 levels to simulate gear, feats, powers, and whatnot. It's probably a bit off, but.. *shrugs* It's attached to this post, if anyone's interested in taking a look.
---
So I had this radical idea at work today - remove turning as a class ability. You can still get it, but only as a domain ability or a feat.
Still with me? Cool. How, you ask, did I come up with this idea? Well... it seemed to me that it made little sense for all clerics to have the ability to turn undead. Sure, I could see clerics of the Sun, Light, Good, etc. domains getting it, and Darkness, Evil, Undeath, etc. getting command/rebuke, but what about all the others? Does it really make sense for clerics of Bacchus, god of wine and partying, to be able to turn undead? Probably not. Matter of fact, in 2E, it specifically stated that the clerics of some gods couldn't turn/rebuke undead. Clerics are already one of the most powerful classes in the game, so removing turn/rebuke undead as a class ability brings them more in line with the other classes.
Paladins, OTOH, always get turn undead - they're paragons of goodness and right, and undead are diametrically opposed to them. They still get it at L4, and are treated as clerics 3 levels lower.
Turning as a domain power: There's already a precedent - the various elemental domains, the Plant domain, and the Moon domain (FRCS). You want to turn undead? Take the Sun domain. You want to command/rebuke undead? Take the Undeath domain.
Turning as a feat: You're not a cleric of the sun god, but you want to turn undead? Take the feat.
Turn/Rebuke Undead [General]
You can turn or command/rebuke undead.
Prerequisite: Ability to cast 1st level divine spells.
Benefit: See turning rules, blah blah blah.
Now, the astute among you might notice that any divine caster can take this feat - adepts, druids, clerics, or that divine whatever class from Complete Divine. Logically, this makes sense:
Adepts - The evil witch doctor with a horde of zombies, or the Indian spirit shaman;
Druids - Undead are abominations of nature. 'Nuff said.
You could give certain divine spellcasting PrCs (or even arcane ones, like the Pale Master) or certain undead (lich, e.g.) the Turn/Rebuke Undead feat as a bonus feat.
As for all those divine feats, you can either a) go the arcane feat route, and have them work on spell levels sacrificed; or b) keep them the way they are, and they're only good if you have the ability to turn undead (either as a domain ability or a feat) - basically, Turn/Rebuke Undead is the first feat in the chain, like Power Attack or Dodge.
---
And while I'm here... some other ideas:
Turning damage: Like I suggested before, turning damage would be 1d6/2 levels, with a Will save (using TR, if any, as a bonus) for half damage.
Turning: Turning (i.e., making the undead/whatever flee) should be kept, simply because undead aren't the only creatures that turning works on. Elementals/plants/lycanthropes aren't unduly affected by positive energy, so it makes little sense to use the energy burst option for them. Yes, I know it says "Turn or destroy xxx creatures as a good cleric turns undead, but let's use a little common sense here, shall we?
Rebuking: I really liked this idea, and it could work for the other creatures as well, not just undead. Both good and evil clerics can rebuke undead. You make a turn check like normal, and all undead in a 30-foot radius must make Will saves or cower, like normal (+2 to hit them). Those that fail their initial save don't get another one; all others must make a save each round they remain in the AoE. You can maintain a rebuke for up to one round per level, and can move up to 5 feet per round, as if maintaining a spell, but moving toward rebuked undead that can't move out of your way breaks the effect on them, and they are free to attack. The effect remains active only as long as the holy symbol is being held up and is visible - casting darkness on the cleric, e.g., would break the effect.
Something else I thought of (random idea) - protection from good/evil provides a +2 bonus to Will saves to avoid being turned, rebuked, or commanded, and magic circle of protection grants +4.