A) Killing something or someone because you think they are evil is evil.
B) Killing something or someone just because you know they are evil, but you do not know about a specific act is evil.
C) Genocide is evil. In general.
D) Killing all relatives of someone on the odd-chance they might come after you is evil.
E) Killing relatives of someone you have a problem with simply because you can is evil.

So, yes. The monster manual stating some member of a race is "usually" (or even "always") evil is not enough to kill them. Doing so is evil in itself.