So let's say Hitler never supports the creation of the Independent State of Croatia, avoiding the Ustaša movement and the genocide on Serbs and other such things. Instead, the place is occupied, just like Serbia. Assuming little else changes (I don't see why it would), how do things play out after the war? Does the fact that the Croats have not tried to ethnically cleanse Greater Croatia of Serbs help Yugoslavia stay together, or at least fall apart less violently?
Hmm this is a very interesting question. Your saying that Yugoslavia AS A WHOLE is occupied by Germany, the way let's say Germany occupied France or Poland etc?
I actually think that Hitler would probably have partitioned the country anyway. Yugoslavia was the created through the hated Versailles treaty which he sought to revise and restore the old order of Europe pre-WWI. So a partition of Yugoslavia was inevitable. Italy would most likely have annexed all of the Dalmatian coast, along with Montenegro and Albania and therefore completely dominated the Adriatic. Slovenia would have been annexed as part of Germany since Slovenia had always belonged to the Austrian half of the Habsburg Monarchy and it was these lands Hitler viewed as historical parts of a Greater Germany.
As for the rest of Croatia and Slavonia I think that in all likelihood Hitler would have re-incorporated these areas into Hungary which was part of the Axis. Croatia had traditionally been a part of Hungary within the Habsburg Empire and it would satisfy Hungarian ambitions of overturning the Treaty of Trianon 1920. I think Vojvodina would also have been given back to Hungary.
Now as for the rest of Yugoslavia and in particular, the Serbian parts of Yugoslavia it is very hard to say what Hitler would do. Macedonia would obviously have been annexed to Bulgaria since Bulgaria was an Axist state and the region of Kosovo would probably be incorporated into Albania which was under Italy anyway. However, the rest of Serbia proper and Bosnia would pose a dilemma for Hitler, since neighboring Hungary and Italy would probably not desire incorporating too many Slavs into their country and would have no interest in these lands.
What I think Hitler would probably do is create a new Yugoslav state in the Balkans involving axis Bulgaria and axis Serbia. Serbia would obviously be massively reduced to its pre-1912 borders, but it would include most of Bosnia which neither Hungary nor Italy desired. Bulgaria would obviously be given dominant status in the union, with Sofia as the capital of this new Yugoslavia. In effect I feel like Hitler would create something equivelent to the Czechoslovak federation involving Bulgaria and Serbia. Just as Czechs were the dominant player in their state, Bulgarians would be the dominant force in Hitler's Yugoslavia with Serbs occupying a similar position to Slovaks in Czechoslovakia.