Literally, as in "Seriously, that is exactly what was written down."
Metaphorically, as in "Why is a raven like a writing desk?"
The problem here is not metaphor, but hyperbole. A statement that is over the top, bombastic, incredulous. Hyperbole often has an aftertaste of rhetorical lies added in. "OMG, I can't believe he actually won that election. Somebody stop the earth, I want off." The person may not actually want to leave the earth, they just dont want to live in the same world that allows things they consider to be bullshit to continue. They definately dont want somebody to actually stop the earth's rotation. It is a kind of metaphor, but not all metaphors are hyperbole. Hyperbole can be a useful literary and rhetorical construct-- it can convey the deeply felt emotional (and therefore innately irrational) status of the person making the statement more effectively than an exhaustive, and highly verbose screed that tries to rationalize it.
If I were to give an etymology of the use of "Literally, she is a douche" type use of "literally", I would ascribe it to a mythological context-- That all actions are preordained by a higher authority. In regards to western culture specifically, where this kind of rhetoric is most common, I would ascribe it to the "book of life" (and or, book of fate) type mythical construct, in which all of one's deeds are recorded. In this mythical tome, it may well be that "She is a douche" appears, making the statement true-- assuming of course, such a mythical object indeed exists. Many strongly believed in this mythical work, which would have provided the necessary linguistic context. "Literally, dude, that's gonna kill you" suddenly has more context behind it than simple misappropriation of metaphor.
That's just conjecture on my part though.
As for the "Loss of use of a word causes a new word to take its place" issue, YES, OMG YES. Just tell that to the SJWs in the politically correct crowd that feel they can eliminate racial epithets by trying to eliminate their literary use-- On some misguided mission to eliminate racial hatreds by removing a means of expression. That new modes of expression will appear to satisfy the need to make the expression held by people with such views, never seems to occur to them, even when pointed out. It bothers me. It boils down to "Nobody is saying bad things now! Racial hatred is gone!" No-- you just gagged all the people you disagree with. That does not make them now agree with you. Different kettle of fish entirely. They will just find a new medium to express themselves, which you will seek to shut down, rather than actually addressing the root of the problem-- WHY they hold the views in the first place. Personally, I would rather that we not end up speaking newspeak just because some people cant understand this, and keep trying to kill "offensive" words.
(Sorry for the derail there.)