There are reasons to avoid using “prokaryote” in biology teaching. So, why are so many biologists resistant to the idea?
Why not use “prokaryote”? Norman Pace published a one-page piece in Nature, “Time for a change” that raised concern about use of “prokaryote” (in education), and the common biology textbook paradigm of splitting organisms up into prokaryotes vs. eukaryotes. Pace highlighted many of the differences between archaea and bacteria, discussed evolutionary relationships/history, and made a case for avoiding use of the term prokaryote with students. (Check out the 2005 article by Jan Sapp discussing the history behind the prokaryote-eukaryote dichotomy, too.) Pace expanded on this with a lengthier educational piece in 2008.