The very same acts are not dealt with by the Fae, so is there a stain or not?
I think that is the question. If Lea kills someone in Chicago, it isn't murder because murder is "the unlawful killing of another human being with malice aforethought, express or implied." The laws of magic, as understood by the Council, are basically "don't do X" with an understood "to mortals." What if there is also an understood "mortals" in front of "don't do X?" It could be that Lea can't do black magic because she isn't mortal. Now there is the question of whether or not a fairy queen is at all mortal and therefore is subject to the cosmic, not council, laws of magic.
"By any other name does a rose smell as sweet?" So an act done by a wizard is soul staining black magic, but the exact same act done by a Fae isn't?
Generally speaking, they don't have a soul to stain, so generally speaking, no.
They are mostly correct because they ignore free will which gives a good approximation of the expected results. The knights of the cross and Uriel look at the problem from a completely different angle. They are all about the importance of free will and want to give the warlock a chance.
In reality each case is different
This is an important point. The Merlin's perspective is that Nature determines actions. The KotC's perspective is that mortal's have Choice (the ability to act against their natures). Uriel makes the point in
The Warrior that mortals almost never exercise Choice. I think Choice vs. Nature is an important theme of the DF.