The cleric's turn undead ability sends undead fleeing, but the wizard's spell Command Undead enables him to give orders to the same undead. What happens when a Wizard uses Command Undead to force a turned undead to keep on fighting (In this case I am specifically thinking of non-intelligent undead, such as a zombie, that will not resist suicidal orders.)? I was thinking that a turning check opposed to a caster level check should be a reasonable way to handle the situation, but is there anything in the RAW that weights in on the matter?
The undead creatures flee until they lose the condition turned
The supernatural ability turn undead inflicts the condition turned (PH 314, DMG 301). In the same way a wizard can't command a creature he dominates to see or turn back to flesh if the creature's blinded or petrified, respectively, a wizard who otherwise controls the turned undead creature via the 2nd-level Sor/Wiz spell command undead [necro] (PH 211) can't command the creature to lose the condition turned.
There are some related terms which you seem to be confusing. Your answer depends on which one you actually intend:
Turn or Rebuke Undead Ability
This is the generic word for the class ability of clerics of all alignments. Also sometimes referred to as "channeling." Confusingly, it encompasses turning, rebuking, and many other effects.
This is the result of a good-aligned cleric using the Turn or Rebuke Undead ability on a relatively strong undead creature. It forces the undead creature to flee.
This is the result of an evil-aligned cleric using the Turn or Rebuke Undead ability on a relatively strong undead creature. It forces the undead creature to cower in fear.
This is the evil version of "turning" undead.
This is the result of an evil-aligned cleric using the Turn or Rebuke Undead ability on a relatively weak undead creature. It forces the undead creature to obey the cleric's orders.
This is the evil version of "destroying" undead.
Dispelling Turning and Bolstering Undead
These are alternature uses for the Turn or Rebuke Undead ability, which make undead creatures no longer flee when turned (dispel), or resistant to turning (bolster).
For more information, see the Turn or Rebuke Undead section of the SRD.
The results of the Command Undead spell will depend on which of the above effects have been applied to the undead in question.
Most of them are pretty simple.
If the undead has been turned (is fleeing), then Command Undead will allow you to issue orders to the target. However, it is still turned, and must continue to flee (and is unable to execute orders to the contrary).
If the undead has been rebuked (is cowering), then Command Undead will allow you to issue orders to the target. However, it is still rebuked, and must continue to cower (and is unable to execute orders to the contrary).
This one is the only complicated case. I recommend looking at the FAQ cited in joedragons answer.
Dispelling Turning and Bolstered Undead
Command Undead has no interaction with either Dispel Turning or Bolstering Undead. It cannot dispel turning or bolster undead. It is not dispelled by Dispel Turning, and Bolstering Undead does not make undead more resistant to Command Undead.
While the sources are different, the type "command" is the same so I'd guess that's the same answer as if someone casts two Dominate Person spells (http://www.d20srd.org/srd/spells/dominatePerson.htm) answered in the FAQ (http://archive.wizards.com/default.asp?x=dnd/er/20070731a):
What happens when multiple creatures dominate the same target? In most cases, both dominate effects would work normally. Each time one of the controllers gives the target a command, the target follows that command to the exclusion of all other activities. As long as the commands don’t conflict, the target simply follows all commands given. The only sticky situation comes when the orders conflict, but that’s handled on page 172 of the PH: “If the controlled creature receives conflicting orders simultaneously, the competing controllers must make opposed Charisma checks to determine which one the creature obeys.”
NOTE: If anyone knows of more specifics of "command" (specifically for clerics as the spell is clear), then this may provide better light and/or a better answer. My reference checks were limited to the SRD and I do not know of any expanded rules/explainations on command undead (thus I didn't consider checking any additional books).
By RAW, the undead will run away. The wizard will still be in control of the undead once it stops running, but the effect of Turn Undead will override that control, at least for a time.
Changing this would not be good. If a necromancer is attacking your party with a horde of undead, then the cleric should be able to turn those undead without having to worry about an extra check to make the turn work. There are already mechanics in place for casters to make turning less likely for their undead (like unhallow or the Bolster Resistance feat), so adding a new layer of anti-turning defense is hardly necessary. In addition, turning typically doesn't work against anything but the weakest of enemies, since most powerful undead have Turn Resistance and lots of HD, which makes them difficult to turn.
In addition, the solution that you propose (turning check vs. caster level check) is very much weighted against turning. A turn check is 1d20+Cha, where a caster level check is 1d20+caster level. Except at very low levels, caster level is almost always going to be much higher than a cleric's charisma bonus, so this would make turning controlled undead very difficult.
No books to quote from, but in most cases for these types of things,"can't" beats "can" for things like this.
Wizard casts Command Undead on a zombie, then demands that it attack the Cleric that Rebuked it. It can't, so it just kinda... shambles around, moaning.
Likewise, Wizard casts Command Undead on a ghoul and demands that it cast Wish to turn the Wizard into a Griphon. The ghoul can't cast Wish, so it just sort of whimpers and acts like a sad dog.
There is plenty of opportunity as a moderator to add your own rule for this kind of situation as long as its fun for everyone. Perhaps a spell check between the wizard and cleric to determine which holds more power over the creature to gain control or maybe the conflicting commands cause the creature to suffer damage, etc...