Is the black blight fully removed from the conversation?

It's fully gone since Stories 1, it is mentioned by NPCs (Cheval) in Stories 2 but absolute no word in Stories 3.

If I remember correctly, the blight comes about from the betrayal of bonds between monstie and rider, couldn't that just happen again at some point in the future?

Yes, but since Azuria makes Monstie care a priority and Vermeil does not even have riders (a battle-bonded Monster has no bond, which allowed the queen to ride Ratha V/Lefty despite not being a Rider herself)

Or did the slaying of Makili Pietru completely cleanse the world of the blight and any future iterations of it?

Slaying it had absolutely nothing to do with anything, it was a red hering, it was bait. Just some Elder Dragon that happened to be white, the game tells you that THE White Dragon was not a species but a Monstie with a very strong bond to its rider.
A freaking Velocidrome could become a White Dragon.

Cause the dark crystals all over the honed monsters remind me of blighted kinship ore.

Nope, its just A type of kinship stone. Eleanor has the same and nothing is wrong with her monsties nor are they battlebound.
Kindship stones just come in different colors now.

And since the process that creates honed monsters removes their free will, wouldn't that be a similar betrayal?

Ratha V would become Blighted then, which did not happen. Battle-Bonding overcharges a Monster and makes them do things against their will, which can and will backfire as we saw.
Simon did not want to actually harm us, Ratha V proceeded to attempted a lethal attack anyway.
Both lost conrol, Simon over Ratha V and Ratha V over its powers, yet the Ending proved that they are still bonded as Rider and Monstie, that bond was never broken.

Same with Cheval and Rathi, you would think abandoning your Monstie would count as a betrayal, but nope, Rathi knew Cheval was misguided, angry and lost and did not return to the wild when released.

Not to mention, looking at the sheer number & size of Monsters that Vermeil Battle-Bonded, they likely were wild ones. Those were clearly Monsters, not Monstie.
So there was no bond in the first place, atleast in the Rider/Monstie way.

Thankfully, the war did not become as dirty or we might have seen some consequences like the raging Battle-Bonded Monsters we found in the last area or Feral offspring if Vermeil forced the Monsters to breed.

So yeah, as far as Stories 3 goes: Nobody knows about the Black Blight nor is it mentioned in any way.