It's genocide of a genetically evil race.
No it isn't.
No way, there is absolutely zero proof in either the OotS canon or the D&D 3.5 RAW (that OotS generally runs on) that Black Dragons are inherently, genetically evil.
Now, in the SRD they are listed as "always lawful evil", but one thing that people keep forgetting is what alignment frequency definitions mean in 3.x, even by the RAW. "Always" doesn't mean "always", it is a game term to mean that the vast majority are evil but exceptions can and do exist.
It's not like they are animated by an inherently malevolent force (like Undead) or have to devour the sentient to survive (like Illithid), or even an alignment-based force made physicially manifest (like Fiends). Chromatic dragons are big magical flying lizards and the black ones may well have bad temperaments and tendencies by genetics (like a Pit Bull) and a racial veneration of an infernal deity (like Tiamat), but they aren't inherently, automatically evil.
Just because adventurers kill things "just because they are evil" all the time doesn't mean it's automatically a good act. There are evil adventurers looking to justify their actions, and there are an awful lot of neutral adventurers that are more after profit and xp and use "it's evil" as an excuse to harvest XP and treasure from monsters in a societally acceptable way. Good adventurers may well kill lots of Black Dragons, but generally in self-defense, or the defense of their town/kingdom/ect and not just stalking them down and killing them in their sleep and crushing their eggs for no reason other than the color of their scales.
As for using anything Miko Miyazaki said as moral guidance with regards to combat (the "color coded for your convenience" crack she once made), look where her attitudes and conduct got her in the end.
Near genocide of a sentient race with free will, even if the majority of them are evil, is still evil.