The problem with Will save is that undead have a good Will save, so this makes them even more resistant to turning than before. Take a ghoul, for example: Will +5. A 1st level cleric with Cha 12 would have a DC of 11 for his turn undead ability, so the ghoul has a 75% chance to resist. If you add its turn resistance +2 as a bonus on the save, it becomes even worse.
Under the core rules, a ghoul is turned as a 3HD creature, so a 1st level cleric with Cha 12 has to roll a 12 or higher to turn it, i.e. the ghoul has a 55% chance to resist.
My house rule is that it's a Fort save (same DC as with your proposed system), and the undead get their turn resistance and Cha bonus (if any) as bonuses on the roll. So, a ghoul would have +3 on the save (+0 Fort, +2 turn resistance, +1 Cha), giving it a 60% chance to resist, slightly worse than in the core rules. However, without the HD dependance, the cleric can now turn skeletons and zombies much easier, which is fine in my book.