Maybe I'm wrong, but I don't recall definitive proof that Beverly was unaware that the Susan Perkins she killed was a clone. I recall an ambiguous reaction or two from Beverly when the real Susan Perkins came to town, but that's it.
It would fit within Beverly's character to "undo" any scientific creation which she felt was ultimately bad for mankind. Killing Susan Perkins' clone may have fallen into that category in her mind -- along with the other reason for killing Susan's clone, which was to permanently keep the clone quiet about The Consortium -- so it was like killing two birds with one stone, so to speak. Since we, the audience, were not yet allowed to know what group Beverly was tied to or what their mission was, the writers couldn't make it explicit that Beverly killing the clone was partly to protect mankind from something it may not have been ready for.
I understand that the clone was a person, too, who in the real world probably shouldn't be killed, but I'm also looking at it from Beverly's potential/fictional point of view. Speaking of which, killing the clone's son may have been something the writers thought about, but didn't take it that far (that would've been too sad).
Also, I don't think Beverly was willing to let them kill Holly or the others. Beverly didn't think it would come to that. She tried to convince Senator Wen that there was an alternative, but it was too late.
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