What happened with literally is not that people didn't understand it's meaning and started using it with some other meaning. What happened with it is what happened with "very" a much longer time ago: it started being used as a generic augmentative adverb and started losing its specific meaning.
When I say "this coffee is so bitter I'll literally die", I'm using literally as an augmentative, as an exaggeration. Similarly, originally when you used "very bitter" it would mean "truly bitter", but overtime it started becoming just a formulaic way of strengthening the meaning of bitter.