This question can be answered in multiple ways -- if you're talking about the Germanization of high culture and politics, the answer is very close indeed. If what you mean is "How likely were the Czechs to go the way of the Lusatians," who I know very little about but who tend to come up in these discussions as a convenient example of Slavs assimilated by Germans, the answer is probably not close, because it's not something anyone was trying to do.

I'm assuming that you're talking about the 18th century or around that time, before the Czech national awakening. This is before the German national movement took off as well, so the Austrian state was not out to turn Czechs into Germans in the same way that national states would later try to socialize members of national, ethnic, or regional minorities into the official culture. (I assume this is what happened to the Lusatians, and essentially what was happening to the Slovaks and others in Hungary after the Ausgleich.) In any case, the Austrian state developed quite a complicated relationship with the German nationalist movement. The measures taken by rulers like Joseph II that contributed to the Germanization of public life and high culture were supposed to serve the purpose of rationalizing and modernizing the state, not stamping out the Czech language or culture. But if all education above the most basic level is conducted in German and the language of state administration is German, the educated classes are going to be speaking and doing their work in German, most books will be published in German, and everyone with political power will be speaking German, so this is obviously going to have an effect on the broader culture.

But these tendencies also spurred the Bohemian aristocracy to support the Czech national movement. The aristocracy rightly saw these reforms as a threat, not because they promoted the German language but because they were intended to centralize power in Vienna, and by supporting nationally oriented intellectuals to establish Bohemian cultural and social institutions, they could counteract imperial influence. Czech nationalists fairly often allied themselves with the local aristocracy over the imperial center during the nineteenth century, which is why the Czechs had an unfair reputation among German liberals and radicals at the time for being a reactionary people.

Also, some of the modernizing forces unleashed (or at least represented by) the same reforms that enabled Germanization also indirectly increased Czech influence. Industrialization brought people from rural Bohemia to cities that had been largely German-speaking, leading to the development of a Czech-speaking middle class, a development that was very important in transforming the Czech national movement from a group of eggheads writing poems and making up words into a real political force. Nationalist activists successfully demanded more space for the Czech language in education and public administration, which ultimately had the effect of turning Austrian state institutions into forces for Czechification rather than Germanization.