First, etymonline says defenestration (and defenestrated) is from 1620 but defenestrate only from 1915. So the simple answer why defenestrate wasn't used before the 20th century is because the word, well, the word hadn't been used before -- it hadn't been 'invented' yet.
Defenestrate may be a bit earler that 1915, here's the earlies I could find, from a 1909 The Athenaeum:
Jehu's command to the Eunuchs to " defenestrate yon luxurious dame " was much appreciated. A new word is always welcome.
Emphasis theirs, and they welcome this new word.
People were never often thrown out of windows, etymonline tells us the term was invented specifically for the "Defenestration of Prague" in 1618 which marked the start of a war. The fact it was also later used to refer to a one or two other similar incidents doesn't mean it happened a lot or that a synonym is needed. The term is now also used to refer to disposing of anything unwanted: "please defenestrate that remark", and at least since 1988 for removing the Windows operating system.
So let's make an Ngram of all these terms:
What's going on here? Why nothing until 1850? Well, Google Ngrams isn't always the most reliable tool. For one thing, not all books are scanned into the Google Books database, especially older ones which are harder to OCR, and not all of the scanned ones are scanned and indexed properly. If we just search for the term "defenestration" in Google Books, the oldest we can find is 1672, very close to the original 1620:
Note two things. First: the word is italic, which suggests it is a new or uncommon word (dum regnabat rosa is italic because it's Latin, for "while a rose reigned"). Second: the 's' looks a bit like an 'f'. (See these two questions for more on this). There are some 17th and 18th century results in Google Books for desenestration and defeneftration.
To summarise: we can't find defenstrate before the 20th century because it hadn't been used yet. The lack of early scanned books and problems with OCR particularly to do with the long-s/f mixup don't help, but we can find defenestration going back to the 17th century in Google Books. For some reason, not all Google Books results show up in Ngram viewer.