I could see two alternative courses the Allies could have taken, if they hadn't put so many chips on the Czech nationalists.
1. No Czechoslovakia at all. Slovakia still becomes independent, so Hungary is still screwed. Bohemia, Moravia and Austria Silesia remains part of Austria, which was IOTL really what was left over of "the lands represented in the Imperial Council" once Poland, Italy, and Yugoslavia got their cut.
2. While Slovakia is independent, Austria gets the German speaking parts immediately adjacent to IOTL Austria in the South, plus that German speaking enclave north of Olmutz (sp?), which is a detached enclave of Austria, the same as Luxembourg was attached to the Netherlands for much of the nineteenth century.
Now #2 is closer to IOTL, and results in a smaller Czechoslovakia and a bigger Austria. But in this scenario, Czechosolvakia keeps the Bohemian mountain ranges. The territory they do lose is to Austria, which is not a threat to them, instead of Germany, which is. The German population within Czechoslovakia is reduced enough that Hitler has less of an issue, though that probably won't make s difference. However, he winds up with the parts added to Austria anyway when he absorbs Austria.
However, #1 makes more of a difference and is probably what should have been done. With Bohemia and Moravia incorporated into postwar Austria, Austria is much bigger, economically more viable, and defensible and has more of an independent identity. And the Czechs make up a much better proportion of the Austrian population than they did in Hapsburg Austria and, though they woudn't get their own country, would still have a major say in how the Republic of Austria was run. The nationalists would have to be happy with that. This probably not only prevents the Sudetenland crisis, it probably prevents Hitler's annexation of Austria as well.