Yes, they are extra to his cleric cantrips.
This is right in your quote:
... you gain two cantrips of your choice from the wizard spell list.
"Gain" is not "substitute".
Yes (arguably), as long as the familiar is delivering a spell that involves a melee spell attack
The relevant section of find familiar says:
Finally, when you cast a spell with a range of touch, your familiar can deliver the spell as if it had cast the spell. Your familiar must be within 100 feet of you, and it must use its reaction to deliver the spell when you cast it. If the spell requires an attack roll, you use your attack modifier for the roll.
This line only applies to spells with a range of "Touch".
The Death Domain cleric's Channel Divinity option, Touch of Death, says (DMG, p. 97):
Starting at 2nd level, the cleric can use Channel Divinity to destroy another creature’s life force by touch.
When the cleric hits a creature with a melee attack, the cleric can use Channel Divinity to deal extra necrotic damage to the target. The damage equals 5 + twice his or her cleric level.
This only applies to melee attacks by the cleric. Since it's not specified, this applies to both melee weapon attacks and melee spell attacks.
One example of a touch-range cleric spell that involves a melee spell attack is inflict wounds:
Make a melee spell attack against a creature you can reach. On a hit, the target takes 3d10 necrotic damage.
Thus, the question simply comes down to whether it counts as the cleric hitting the target if their familiar is delivering the spell.
Since find familiar specifies that "If the spell requires an attack roll, you use your attack modifier for the roll", I'd argue that they're functionally equivalent. Thus, I'd rule as DM that any melee spell attack delivered by the familiar that hits qualifies for Touch of Death.
The counterargument
Of course, the reverse argument could be made, too. The familiar delivers the spell "as if it had cast the spell", so one could argue that aside from using your attack modifier, it's as if the familiar made the attack - and thus argue that if the familiar delivers a spell, the cleric is not the one making the attack so they can't use Touch of Death.
It's ambiguous, and could be interpreted either way. Thus, the DM and players should come to a ruling that makes the most sense to them, and be consistent with it.
Best Answer
You use your (Wisdom) Spellcasting Ability, and the cantrip counts as a Cleric cantrip
Since the text doesn't explicitly say to count the spell as a Cleric spell, the first thing we need to do is consider the counterpositive: What if we asserted that it wasn't a Cleric Cantrip when learned through this feature?
Well, we couldn't rule that the spell must use Charisma (as though learned by a Warlock or Sorcerer) or Intelligence (as though learned by a Wizard) because the rules don't give us a way to decide which we would use. Chill Touch is not a "Wizard Spell/Warlock Spell/Sorcerer Spell", it's "A Spell that appears on the Spell Lists for Wizards, Warlocks, and Sorcerers". There's no intrinsic property of a spell that makes it a "[X-class] Spell", that terminology is just colloquial jargon (and not formally defined at all) for "spells you have learned as a [X-class]".
Furthermore, the Cleric class doesn't give us a way to use Intelligence or Charisma as our Spellcasting modifier. These are properties of the Wizard and Warlock (and Sorcerer) classes, levels in which the Cleric has (for the purposes of our example, assuming a single-classed character) not taken.
So if a Death Domain Cleric were to learn this spell through a Cleric feature, the fact that it's neither on their class list nor a "Domain Spell" is irrelevant: you learned it as a Cleric, and it doesn't make sense to treat it as anything other than a Cleric Spell. You therefore use your Wisdom ability as your Spellcasting modifier for this spell, same as any other Cleric spell.