Let's see. It's not happening in 1805, right after Austerlitz because the Russians are still at it and the Prussians are looming on the horizon.
But! In 1809, Napoleon could be very irked. That's twice the Austrians have frustrated his campaigns (yes, there was no way he was going to successfully invade England. Still, it had to rankle). They have prevented him getting his way in Spain, or at least that's how he sees it. He has been wounded. He has even been defeated at Aspern-Essling. Lannes is dead. Wagram was a bloody mess. So, for a POD, let's assume that Friedrich Staps makes his attempt on his life before the Treaty of Schönbrunn is negotiated and actually wounds him. Furthermore, Staps is rumored to have had been egged on by some Austrian aristocrats, possibly a member of the Imperial family. Napoleon is now good and properly pissed.
So he takes all the Provinces Illyriennes as per OTL from Austria for a start and then some (4, 5, 7 and 17). He takes Venice and the surrounding area for the Kingdom of Italy (19). 10, 13 and 15 go straight to his ally Bavaria. And now Napoleon is really hitting his stride. So he eyes Galicia and the remnants of Silesia and decides that with Austria and Prussia properly humbled, he can afford Russian hostility: 2, 6 and 11 go into Poland's pot. And then, for good measure, he splits Hungary in two and creates an 'independent' kingdom consisting of south 16 plus 18 and 20 which he gives to his brother Louis who gives up his throne in Holland (annexed into the Empire proper a year ahead of schedule).
The remnants of Austria are now encircled to the north by a resurgent Poland, to the east by Hungary, to the west by Bavaria and to the south by Italy and the Empire. It keeps only 1, 8, 9, 12, 14 and maybe 3. Its army is reduced to 100, 000 troops with several French divisions staying to make sure there is no monkey business about it. If there is the slightest whiff of talk with Britain, Napoleon makes it very clear that Bohemia and Moravia will go straight to Saxony and this time he will forget to be nice.
Satisfied with a good afternoon's work, Napoleon goes bride-shopping, since Marie-Louise cannot possibly be of use to him (except as a potential mother of his children), considering the utter ruin of the Hapsburg-Lorraine, before planning his next strike in Spain.
It's not very likely. But unless Austria is dismembered until it's no bigger than it was before the Renaissance, it will always be a stumbling block to Napoleon on the continent. Unless it's given the Prussian treatment, it will rise again (and even then, Prussia managed to throw off the yoke after the disaster that was the Russian campaign).
Edit: also, except for 1812 and the lead-up to Leipzig the next year, I would not say that Austria was traitorous, per se. It just so happened that its interests kept clashing with France's and Napoleon's.