I agree that this stuff can be a complete headache. Hate it when balanced rules throw me a power curveball. Yes, Tome and Blood - I'm looking at you and your
Persistent Metamagic.
Could you sit down out of game with the cleric character, explain the problem and get him to re-tool his character without some of the problem items/powers? He can keep an undead killer focus, but pick up something else as well...
Some players might go for that, although it could kill the game for others.
If it's an in game fix...
IIRC, a Death Knight is immune to turning...
A player can't turn what they don't know is dead. Ex - a BBEG could pretend to be human/demon/etc? A combination like Mind Blank/Nondetection and Disguise Self could work - they may be able to see through the disguise, but still can't make out what's under there? A smart BBEG could even leave clues leading to the 'wrong' answer.
The simple lich is good for this - even if they get destroyed, it's a quick return trip to their portable home! Then back again 24 hours later. My PCs learned to really hate these guys in 2nd ed days!
Even better, something like Piratecat's Soder BBEG - with 'corpse mobility' - current body blown up by turning (or spellcasting!)? Time to hijack another one.

He seems able to do this even more than a lich and is far too cool!
Keep undead minions so the cleric can showboat, just don't use undead BBEGs with low hit dice...
Turn it into a plot point for a while - undead are swarming the land - turning has gone unstable - it still works most of the time but it's having strange side effects - plagues of locusts, rains of blood? And it's getting worse. Why has the link to the positive energy plane been disrupted? Who is responsible? Aaagh, the sky is falling. Etc.