No, this is dreadful, and she (and you) deserve to be called on it because it robs us of the ability to understand the parallels.
Unless you think race is deeply meaningful biologically, one set of distinctions is no better or worse than another. What matters is how the distinctions are used by the people in positions of power.
The Holocaust, and the associated racial genocides of other groups by the Nazis, are the clearest and most terrifying example we have of the immense dangers in the ideas of racial superiority and racial cleansing. If you draw the boundaries in different places, it's still just as scary.
Whoopi's comments rejected as irrelevant the critical lesson we should learn from this atrocity. It's not any old kind of inhumanity. It is precisely the kind of inhumanity arising from my-race-is-better-than-yours. Obfuscating or denying this deserves no applause whatsoever.
However, a simple correction is plenty: yes, the Holocaust was about race because that's how the Nazis viewed race, and they were the ones doing it. People make mistakes; we are better off if we let them quickly fix them and get on with what they're good at.