This is not a new phenomenon; I think we've been able to cope in the past by either clarifying precision by context or adopting new words with the precision we need until they get watered down as well.
> literally is commonly used to mean not literally
I realize at least one dictionary disagrees with me, but I think that's a mistaken analysis of the phenomena. Literally is quite frequently used as an intensifier even when the utterance is meant figuratively, but if it were left out the utterance would not be intended or interpreted as more literal.
I think what is happening is that "literally" is being used as hyperbole, much like any other bit of English can be. It doesn't mean "not literally" in the same way that when someone says "you left me waiting for days" we don't say "days sometimes means minutes" and fret about how anyone will ever measure time again; we rather say that people sometimes exaggerate. None of this, of course, should prevent you from objecting to this use of "literally" on stylistic grounds, or from objecting to individual confusing utterances of any sort.
> Given the rate of mutation and transmission in bugs with natural gestation and migration, the probability of catastrophic outcomes is exponential without a similar dataset in other human food sources.
Freud and Jung used the term unconscious (das Unbewusste) - it is probably not a recent trend.
Basically, just because the words are constructed the same, doesn't mean you can translate one direct part-by-part into the other.
For a similar example of the principle that logical structure doesn't translate naively one-for-one:
"Du darfst schlafen." <-> "You may sleep."
"Du musst schlafen." <-> "You must sleep."
"Du darfst nicht schlafen." <-> "You must not sleep."
"Du musst nicht schlafen." <-> "You may not sleep." [Though this last one is ambiguous in English.]
It’s similar to how unconscious is now commonly used to mean subconscious (i.e. not unconscious) and literally is commonly used to mean not literally.
It troubles me that our specific words are getting watered down by pop usage, like sharp tools being blunted. This is different than my usual prescriptivist screeching.