Killing Hitler won't end World War II. There's way too many factors fueling World War II, and remember, up until about half way through, it looked very much like Nazi Germany was going to win big.
The Nazi party had full governmental and ideological control of the country. The atrocities being committed here kept under wraps; most German citizens lived a normal life, unaware of the campaign of terror being waged against their neighbors.
Hitler was the charismatic leader who organized the party, and he was definitely the Fuhrer. The concept of Führerprinzip pretty much made him de-facto dictator for Nazi Germany. But it didn't make Nazi Germany depend on him.
Depending on when you kill Hitler, it's much more likely you'll help Germany win. For a huge part of the war, Germany's "Lightning War" was doing just fine. They'd negotiated a peace with the USSR, they took over most of the mainland of Europe. America was still sitting out the war with its untouched factories and untapped industrial power. Imperial Japan was chewing their way through the Pacific. It looked like Springtime for Hitler, and Germany.
But the problem was, Hitler was insane, or was slowly slipping into insanity. He became paranoid, turning the terror of the regime on the upper crusts. He was burning billions of reichmarks on failed projects, and constantly demanding "wonder weapons" that would swiftly end the war with total victory. His initial reticence to bomb Britain had been blown away, and he took the Battle of Britain personally. He was the one who pushed the military into a two front war, during a time when the new Reich was becoming exhausted.
If you kill Hitler in the middle of the war, all you do is ensure German victory. Cooler heads would have prevailed, the regime would have softened up a bit, a truce would be called with Britain and lucrative trade deals set up with America. Japan would be convinced to satisfy themselves with the Pacific and not poke America, at least until Germany firms up its grip.
The last thing you want is a wonderwizard to step in and kill Hitler.
Killing Hitler before World War 2 wouldn't stop the National Socialists, or the war. Hitler was a key recruiter for the Nazis, and was deeply involved in the symbolism and pomp of the Nazis... but he wasn't indispensable. When he first joined the Nazis, it was as a spy and an informant, loyal to the government. It was by attending these meetings that he became radicalized, but not too radicalized. But remember: It was the men around him at the top, running propaganda, organizing the SS and the death squads, who actually made the Evil Nazi stock character possible. Those people would still have migrated to the party, and who knows where that would lead.
A startling number of people were, willfully or not, ignorant of just how totally evil the Nazis were. There were Nazi supporters here in America, even through the first stages of the war. When reports of the concentration camps came out, most people refused to believe it. When soldiers SAW the concentration camps, they refused to believe it. Surely nobody could be THAT evil. With the ability of hindsight, we can see that defeating the Nazis would be an imperative, but from their point of view... they might not realize it until it's too late.
My best guess is that the Wizarding community took a glimpse into the future, got some prophesies, and noticed that everything they tried to promote peace ended up worse than the WWII that we got today. Kill Hitler, and Germany doesn't lose; that's a pretty good reason to not kill Hitler, and it's a pretty good reason to make sure no wizards interact with the war.
Considering Germany's Wonder Weapons, and the huge leaps and bounds in technology that came from the war, are we sure no wizards participated? They just wore lab coats or tweed jackets and participated in the research and development. Figuring out the V rockets, or setting up "RADAR." Or using their skills to become an ace in the skies of Britain during the Blitz. They dare not use their powers in the open, or else they'll be taken by their own governments and torn apart to figure out how they work... or worse, they'll be used for those very missions they need to avoid turning the world on its ear.
I can imagine Churchill thumping the desk in the Ministry of Magic demanding to know why the wizards haven't sent squads of soldiers into enemy territory, and being told that the wizards have their own mutually assured destruction; as long as all wizards stay OUT, everyone will stay out. But if any side is seen to be assisting their side, the other side's wizards will support their side as well.
And it won't be wizard against wizard; it'll be wizard against fleets, wizard against army battalions, wizard against entire air force wings. Their force is so strong, they won't be competing with each other, they'll be decimating the muggles. And even Churchill would have to consider the repercussions of that.