You definitely want to use 1/2 HD in that equation, not HD.
Even so, you're going to end up with a situation where non-intelligent undead are harder to turn than intelligent undead (and that's ok, if that is your specific intent-- I'm just trying to help you avoid unintended consequences).
Non-intelligent undead get about 3 HD per 1 CR; intelligent undead can be as low as 1 HD per 1 CR. In fact, the more the undead feels like a "boss" with all kinds of special abilities (vampire, lich, mummy) the lower its HD:CR ratio will be.
This is why we tied the mechanic to the POOR Fort save for non-intelligent undead (1/3 HD) and the GOOD Will save for intelligent undead (2 + 1/2 HD).
If you're going to go through the trouble of creating a "Turn DC" for every creature (and it's really not that much trouble-- I'm warming to the idea), then I recommend 10+Will save for intelligent undead and 10+Fort save for non-intelligent undead (plus turn resistance if they have it).
And the cleric PC's check should be 1/2 cleric level + CHA.
When I say "should be" 1/2 HD, I mean, "Should be if you want it to work the same way the core mechanic does things, and keep the d20 roll valid."
And you should never undertake any revision of turn undead without keeping the following fact in the back of your mind:
The grey render zombie has 20 HD and is only CR6.
It really helps keeps things in perspective.
This is extremely useful information. Thanks so much!