I'd regard what you're calling "historical" as being the actual standard usage in conventional speech -- again, I've never encountered the notion that "prosecute" doesn't apply to civil litigation until today, and I've been speaking English for decades, and have had many discussions involving legal cases, conversed with lawyers, signed contracts, etc. throughout my life.
The fact that you're referring to an intra-disciplinary dictionary to make the opposite argument implies that the narrower definition is jargon, and not an accurate representation of the common meaning of the term.