Holocaust deniers for the most part don't claim that it was entirely fiction. What they do is say that the numbers and intention were exaggerated, that World War II was a tragedy all around and the holocaust happened in the context of a war in which lots of people were killed. In other words, yeah some people died but it wasn't the big deal everyone makes it out to be. And, that's precisely what Gibson said to Peggy Noonan:
I have friends and parents of friends who have numbers on their arms. The guy who taught me Spanish was a Holocaust survivor. He worked in a concentration camp in France. Yes, of course. Atrocities happened. War is horrible. The Second World War killed tens of millions of people. Some of them were Jews in concentration camps. Many people lost their lives. In the Ukraine, several million starved to death between 1932 and 1933. During the last century, 20 million people died in the Soviet Union.
As David Neiwert wrote:
It's important, of course, to understand that this is exactly the storyline pushed by Holocaust deniers, namely, that yes, there were many Jews killed in Europe during World War II, but they were only a small part of the total who died in the war, and the "6 million" number is grossly exaggerated. Not only is this exactly what Hutton Gibson told the New York Times, you can find the exact same views at such Holocaust-denial organs as the Barnes Review, the Institute for Historical Review, and the Adelaide Institute.
There's no conflict between creating a miniseries based on a novel which takes place in the context of the holocaust and being what we call "holocaust deniers."