The diplomacy hit for erasing a civ seems to vary a bit. If the civilization you destroy is universally despised and you are already well-liked (or feared) the penalty may not be as big. In my recent science victory as China (Emperor, Epic, no AI personality mods) I wiped out multiple civs on my home continent and Gandhi, of all people, remained my friend. I think he popped up once and scolded me, but he didn't actually denounce or turn guarded. He even engaged in some genocide of his own, wiping out the last German city after they declared war on him.
Eventually Gandhi turned on me, but that was only after I was the clear runaway and had absorbed every other nation on the continent. Similarly, Suleiman on the other continent was friendly with me for the entire game, until we were the only ones left. Then he denounced me, warning.....no one.... that I was not to be trusted, and I launched for Alpha Centauri shortly thereafter.