True, but it's not the first nor the last time this will happen.
Divining why the idiomatic usage of words changes over time may be a gainful occupation, but I would suggest there is no way to prevent the process altogether. Even "classical latin" has been amended with neoclassical adaptations and back-formations. (Even Attic Greek was transliterated / adopted into latin, so it is not a new process.)
Nevertheless, if I were to hazard a guess as to why the definition of "irony" is changing over time, I would resort to lexicographical Darwinism: the word was atrophying and another use was foun for it. The word fits into people's Weltanschauung better as verbal irony, and this is used to differentiate from hypocrisy (maybe because the potency of hypocrisy is waning and another totemic word needs to be invoked to convey the same gravity?). Incongruity, methinks, is under the shadow of the mathematical term "congruent", and has too much baggage for arts majors to use in conversation ... :D