Well, this morning I did bump it to d6 per level, to get it more on par with how it works in core (in terms of what level you need to be to be able to expect to destroy an undead creature).
Perhaps I should change it a bit. I do like the idea of positive energy always healing living creatures, so maybe is should be more like this:
Turn Undead
You create a burst of positive energy centered on yourself with a thirty foot radius. All undead creatures in the area take 1d6 points of damage per Cleric level. All living creatures in the area are healed for half that amount. You are not affected by your own turn attempts.
Bolster Undead (replace rebuke undead)
You create a burst of negative energy centered on yourself with a thirty foot radius. All undead creatures in the area are healed 1d6 points of damage per Cleric level. All living creatures in the area take damage equal to half that amount. Living creatures may make a Will save for half damage (DC 10 + 1/2 Cleric level + Cha mod). You are not affected by your own bolster attempts.
Improved Turn Undead
Prerequisite: Ability to turn undead
Benifit: When you turn undead, all undead creatures in the area must make a Will save (DC 10 + 1/2 Cleric level + Cha mod) or be paralized for a number of rounds equal to half your Cleric level plus your Cha mod. This ability bypasses an undead creature's normal immunity to paralysis.
Rebuke Undead
Prerequisite: Ability to bolster undead
Benifit: When you bolster undead, all undead creatures in the area must make a Will save (DC 10 + 1/2 Cleric level + Cha mod) or risk falling under your control. If your Cleric level is at least double the undead creature's hit dice and it fails its Will save, it is under your mental control. You may control any number of undead creature's whose total hit dice does not exceed your Cleric level.
Analysis: The damage from turn undead above scales well in that each cleric level deals roughly 1/2 an undead creature's hit dice of damage. Thus, every two cleric levels will deal one hit die of damage to an undead creature on average. Taking the Will save out keeps this consistant. The positive energy heals half this amount to living creatures, but I'm excluding the cleric. The biggest reason I excluded the cleric is I didn't want the boster ability to damage a cleric. Of course they could take Tomb Tainted Soul, and it would be quite worth while. Should this affect the cleric too?
The bolster ability heals an identical amount to turning damage, so they cancel eachother out nicely. Should the bolster allow undead to gain temporary hit poitns? If so, I would want to cap it (perhaps one hit point per hit die, or something like that). I used the name bolster because I thought it was more descriptive. I suppose I could change this back to rebuke to be less confusing...
I decided to go with paralysis instead of fear for the improved turning. I did this both because if you have to spend a feat to get it, it should be worth it, and also because it's a pain in the ass to track down fleeing undead. Also, they're immune to crits, so you can't just go CDG them.
Hopefully the mechanic for rebuking (controlling) undead is good enough.