If Germany did no wage a war against the Jews they would have probably developed the A Bomb first there by securing the thousand year riech.
I wouldn't call it so much a 'war' as 'industrial slaughter'.
Thunderhawk aptly underscores the main problem(s) with this 'what-if' question of the War without the Holocaust. The Jews of Europe left that continent for the discomfort of the standard antisemitism of Europe. So even if the Nazis were not rounding up Jews (and other minorities in the millions) and destroying them, it difficult to say that none would have left and all (scientists, engineers, etc) would have complied with a totalitarian Nazi State. Secondly, removing the virile antisemitism of the Nazi 'platform' would be voiding a mainmast of their party, thus undercutting their efforts to gain power.
The Germans developing atomic weapons with the help of the Jewish scientific community is dubious in itself. To be sure, it is also problematic since the Germans were under siege at almost every crucial juncture in the war on most fronts, particularly in the air, making it quite difficult to manage the all the processes, collect the already limited resources, and construct the then most complex weapon in history. Even under ideal, peaceful conditions in Nevada, the Americans took some four years to get it right.
Another reason one could doubt that the Nazis could build atomic weapons during war time was the simple problems of the Nazi state. Despite the myths of 'German ruthless efficiency', the Nazi war and peacetime state was an unwieldy and poorly run. In fact, it was more akin to a collection of power centers (though all loyal to Hitler) that competed viciously for more power. Had atomic weapons become more of a real possibility for the Germans, this new scientific power would have been a seen as the crown jewel of high level Nazis, such as Goering, Goebbels, Himmler, and so on. The result would have been infighting and personal (and perhaps real) sabotage to gain this new power. Hitler was notoriously aloof (often encouraging these intra-Nazi Party Struggles) and would probably not settled this sort of dispute. The result would have been even more delays to a German atomic program, and (assuming the Germans are still at war with the Russians and the Allies) time would have likely run out on the German Atomic program, as it did in real life.
Finally, I doubt that an Atomic Bomb, and the possession of the atomic bomb would guarantee the Third Reich one thousand years of existence. The Soviet Union, by the mid 1970s, had more nuclear tipped ICBMs then any nation on earth, perhaps the most powerful force in human history. This force did nothing to save the Soviet Union in the 1990s. In fact, it probably considerably helped the process of the Soviet Union's demise.
Anyway, Nazi Germany may have been able to buy itself time with atomic weapons, perhaps even force peace with the West and hold the Soviets back at the Elbe. But, by 1944-45-46, if the Germans were able to develop a bomb by that time, a time when the Luftwaffe was but a minuscule shadow of the force that battled the RAF and mauled the Red Air force, and when the Allied and Soviet Air forces have complete air-supremacy, it would have been extremely difficult for the Germans to deliver a bomb to London, and nearly impossible to Moscow. Pairs maybe.
One may contend that the Germans might have used the V2 as the delivery vehicle. But by 1945, (the earliest at which I think the Germans could have anything to show for their atomic program) V2 launch sites were being bombed or captured by the Allies.
In short, I'm not so sure the Germans could have developed a bombed, even with the help of the Jewish scientific community, in time to save their regime. And even if they did, I'm skeptical if they could have delivered it in time by the waning years of the war.