German unification was rather recent, at least more recent then Austira control over Hungry. Why did the allies keep Germany unified during the peace process?
Surely it would have been easy to break Germany into several lesser states and ensure both peace while preventing Prussian consolidation of power.
Germany did not surrender unconditionally at World War I. The Allies could not just do as they pleased. There were not Allied troops on German territory, they did not have any way of seizing control over Germany. What they could do was first setting up a truce (Armistice of Compiènge) and later a peace treaty (Treaty of Versailles). You needed someone German to sign both of those, and you needed Germany to be intact to do so. If you'd want Germany to split up, you'd need every single one of those new states to sign that treaty.
I am not very familiar with Austro-Hungarian history and their subsequent break-up after WWI, but I don't think it has so much has to do with the Entente, as it does with an ethnically fragmented empire falling apart.
But in regards to Germany, as far as the Entente was concerned the Germans were still able to put up one hell of a fight, even after fresh American troops came pouring into France! There is plenty of evidence for us today to analyze and see that the Heimatheer (troops in Germany) were unrealiable, the Eastern Garison force dispersed and maybe radicalized, the Etappe (hinterlands behind the Western Front) was a mash of shirkers and revolutionary troops. We can know that today, at the time to the Entente the Germans were just unbelievably tough fighters, who would surely fight tooth and nail on their on soil.
The Officer's Corps on the front lines was never broken and of the roughly 1.5 million troops still stationed on the front, they had many opportunities to desert or avoid front action, but they didn't. Take some other numbers into consideration too: 20% of the population served in armed forces in a 4.5 year period (13 million troops), over 2 million died, hundreds of thousands starved to death or became sick due to malnutrion at home, yet it is estimated that only 50,000 troops deserted, most at the end of the war! The German army also consistently captured or killed more British and French troops in every battle than their own suffered from enemy hands. They managed to fight a two front war, placed in the center of Europe, tame the Russian Empire, and mount a huge offensive in 1918 almost taking Paris!
Now imagine yourself in 1918 on the side of the Entente. In September you hear word that the Germans may be willing to negotiate peace, you have lost millions of men, you have had 4.5 years of the worst war in human history, you know any post-war world will be difficult to manage with your immediate neighbor, who will continue to be your sworne enemy. Do you..
A) Continue the war using foreign troops (because your army is on the bring of mass desertion) invade a country, topple the government, and reform it entirely without anything functioning domestically?
B) Force the obviously losing country to sign an Armistice, demanding for their immediate withdrawal of all foreign nations and then send your completely exhausted army to occupy foreign hostile terrority, while you figure out how to repair not only your own government, economy, and army, but an ENTIRE other country's?
C) Force the obviously losing country to sign an Armistice, demanding for their immediate withdrawal of all foreign nations, set up an occupied and neutrel zone not far away from your own borders and begin working on a treaty with the complete upper hand?
C was really the "best" option. I could probably add more and if you have any further questions, I will be happy to fill in gaps.
I hope this helped