Does it basically mean "don't compare because it's different"?

It's like a schoolboy calling their teacher a Nazi for putting them on detention. There's an abstract point of comparison (authoritarian behavior), but the differences in scale, severity and underling motivation are so vast that the comparison is absurd. If someone seriously wants to argue against this particular form of affirmative action – and knows what South African Apartheid actually was – then they don't make this comparison.

(Similarly, if you think a teacher is being too authoritarian with their students, you won't make your case any more convincing by making comparisons with crazed dictators.)

You could have saved a lot of words there by just writing "your opinion isn't valid because I say so"

Not really, because I wasn't arguing against the poster's opinion (as I don't know much about, or have strong opinions on affirmative action in New Zealand), but only the absurd comparison being used to support their argument.

Calling people nazis is ok though?