I like the idea of making him an assassin. I mean he is a Witch HUNTER. Not a Witch "I'm going to calmly approach in a ranked unit and take my time to kill you." This guy should be darting in and out of forests, jumping from roof tops, tracking the movement of heretics!
M 5 WS 5 BS 5 S 4 T 4 I 5 W 2 A 3 LD 7
A Witch Hunter always comes equipped with Light Armor, and a Shrouded Cloak, giving him a +3 save against shooting attacks and +1 against close combat attacks.
Works Better Alone: A Witch Hunter may never join a unit.
Old Parlor Tricks: The Witch Hunter refuses to admit that he is susceptible to magic, and therefore, cannot be affected by spells, neither from a friendly source nor from an enemy.
Hunter's Instincts: The Witch Hunter has hunted evil for decades and has developed super natural instincts. The Witch Hunter benefits from a 5+ ward save. The Witch Hunter benefits from being a Scout.
Been There, Done that: The Witch Hunter never has to take fear checks that would be required when fighting Undead or the forces of Chaos.
Different Job, Different Tool: The Witch Hunter comes may chose to specialize in the hunting of certain models, and is equipped accordingly
The Undead: The Witch Hunter comes armed with the Crossbow of Smiting, Holy Water, and a Blessed Mace.
Holy Water: One use only. When engaged in a combat with an undead oponent, but before either side attacks, the Witch Hunter may declare that he is using his Holy Water. Every model in the front rank of the undead unit suffers a strength 5 hit with no armor saves allowed. Ward saves and Regeneration Saves may be taken as normal. Characters do not benefit from "Look out, Sir!"
Crossbow of Smiting: This crossbow is rumored to have been blessed by Sigmar himself. The crossbow can never hit on worse than a 4+, and may single out characters. Note that when targeting characters in a unit, you still suffer the -1 penalty, but this cannot make you hit on anything worse than a 4+. Resolve attacks from the Crossbow of Smiting as a bolt thrower as described in the rulebook.
Blessed Mace: Against undead, the Blessed Mace counts as a "poisoned" weapon. Against all other opponents it still counts as a magical weapon.
The Heretic (Chaos): The Witch Hunter comes armed with a Modified Repeater Pistol, Blessed Blade, and a Prayer Book.
Modified Repeater Pistol: The Modified Repeater is of Emperor design, but with the craftsmanship of a Dwarf. As such, the Modified Repeater Pistol is treated as a Repeater Pistol as described in the Empire rulebook with the following changes: The Modified Repeater Pistol can never hit on worse than a 4+, and may single out individual characters. Note that when targeting characters in a unit, you still suffer the -1 penalty, but this cannot make you hit on anything worse than a 4+. The Modified Repeater Pistol has a range of 12" rather than 8".
Prayer Book: One use only. At any time in the magic phase, the Empire player may declare that he is using a Prayer Book. All Chaos units within 12" of the Witch Hunter take 1+d6 strength 5 hits with no armor saves allowed.
Blessed Blade: Against Chaos opponents, the Blessed Blade counts as poisoned. Against all other opponents, it still counts as magical weapon.
The Wizard (any spell caster): The Witch Hunter comes armed with "The Silencer", a Companion Dagger, and the Invisibility Cloak.
"The Silencer" is a magical dagger that has been used to cut many a spell short. The Silencer may be used as either a throwing weapon, resolved as a pistol, or as a close combat weapon. As a ranged weapon, the Silencer will always hit Wizards on a 3+, regardless of modifiers. The Silencer may always target a Wizard even if some other rule would normally prevent him from doing so. Against all other targets normal shooting penalties apply. Such is the magical nature of The Silencer that should any Wizard be wounded by the dagger, he may not cast a spell for the remainder of the game, nor will he generate power dice nor dispel dice.
One use only. The Invisibility Cloak is an enchanted cloak that the Witch Hunter has picked up off the corpse of a mighty Archmage he has slain. Once per game, in the Empire player's movement phase, the Empire player may declare that the Witch Hunter is using his Invisibility cloak. Until the next the next Empire player's turn, for all intents and purposes, the Witch Hunter does not exist. Units may move through him and may not target or inflict harm on him in any way. Should the Witch Hunter attack while the Invisibility Cloak is active, he will cease to benefit from being Invisible.
In close combat, the Companion Dagger may be used with "The Silencer" to generate an additional attack that is resolved as if from the Silencer.
I would have this guy cost 75 points base. The Undead kit would cost 65 points, the Chaos kit 50 points, and the Wizard kit 75. I think these points are right more or less.