Devil's Advocate: It would be wrong, but we may have saved ourselves a bit of a headache today...
Hitler killing Muslims by the millions would do the exact opposite of stopping radical Islam, you would instead be seeing its rise decades earlier than in our timeline in an even more violent form. The only way you would not leave an incredibly angry Muslim population behind after this (there were Jewish movements who wished to make Germany suffer for the Holocaust and the Allies were seriously entertaining the idea of leaving Germany as a medieval society to punish it, with only the Cold war stopping this idea from being implemented, so I sincerely doubt that Muslims would not entertain ideas of revenge on Germany) is if Hitler made some magical death ray and somehow killed
If Hitler had eased off on the Jews, would 20th century xenophobia instead be defined by what Japan got up to during World War II? Because the highest estimates say Hitler had 6 million Jews, Romani and other such "undesirables" killed, but the highest estimates put the Japanese kill tally at 10 million Chinese, Korean and various other Asian groups. Between that and doing their level best to try and turn China into a giant rape camp, I'm always surprised the Nazis get more (deserved, certainly) flak for World War II than Japan did. Maybe it was the nukes.
The entirety of the European/African theater added up to 21,800,000 to 28,000,000 dead in the Soviet Union alone, about 800,000ish thousand dead from America and the U.K, 1,027,000 to 1,700,000 dead in Yugoslavia, 5,620,000 to 5,820,000 dead in Poland, 7,000,000 to 9,000,000 dead in Germany, 580,000 dead in Hungary, 320,000 to 807,000 dead in Greece, 88,000 dead in Belgium, 550,000 dead in France, 100,000 dead in Ethiopia, 454,600 dead in Italy, 800,000 dead in Romania, 325,000 dead in Czechoslovakia, and I'd keep on going but this is hella depressing and basically thanks to Hitler; pretty much every country in Europe that didn't completely sit out of the war was left a charnelhouse. In total some 46,000,000 people at the highest estimates had died of preventable causes due to the war.
Japan's romp in Asia is responsible for the deaths of up to 10-20 million Chinese, 3=4 million Indonesians, 1.2-2 million across Indochina, 0.5-1 million Filipinos, assorted other Asian groups who add up to about 1 millionish total. 2.6 million to 3.2 million Japanese people also died, several million throughout the British Raj perished, and so on so forth. Up to 41 million died in the Asian theater.
I'd say even without the Gas chambers being a thing, Hitler's Germany would still be remembered as basically the worst thing to happen to Europe thanks to the Wehrmacht and SS's incredible brutality and starvation policies (Germany had a pretty crap agriculture system so they planned on starving most of the rest of Europe to keep themselves fat and happy), its barbaric treatment of POWs in the Eastern Front and cartoonishly villainous methods of dealing with partisans, as well as setting many macabre records for massacres by gunfire.
Japan was by all means, incredibly and unimaginably brutal and sadistic, but whereas Japan made an art out of mass murder, Germany made it into a Science. I think this is ultimately why we find Germany the more abhorrent of the two. It was more than just barbarism, it was taking all the tools of "civilized" and "enlightened" society and turning them towards goals that nobody seriously believed that European people were capable of pursuing. Meanwhile given the racism at the time it was considerably easier to swallow the idea that Japan hit Asia the same way Syphilis hits your genitals.
Sauce for casualties: http://en.wikipedia.org/wiki/World_War_II_casualties
As for the thread topic, I'd say that this stinks of hilariously transparent Islamophobia. In fact, I'm gonna go ahead and say that