I doubt that, a surviving house of Hohenstaufen would remain one of the great houses, so they will get elected as HRE at various points. They could lose their de facto hereditary position though. The house of Hohenstaufen might not even die out, their great rivals the (younger) house of Welf managed to survive.
Furthermore Swabia will survive as a duchy, no great interregnum and emperors more focused on the HRE, this could benefit the cohesion of the empire.
This will also have an effect on the Habsburgs and the (Limburg-)Luxembourgs, it is very unlikely that they will be as successful as IOTL, but some emperor might (or might not) still reward them for their services.
It will also have interesting results for the kingdom of Sicily and on the Italian peninsula. I can see Sicily expand in similar way as Aragon IOTL; and Sicily might gain Sardinia & Corsica, but the main focus will probably be towards the Eastern Mediterranean.