Take Khan out. Take genetic engineering out. Harrison is just a starfleet bad guy. Fandom would proceed to complain about the Insurrection ripoff.
No, they wouldn't. For one thing, there really wasn't a star fleet bad guy in the movie. Just your typical well meaning but completely mislead admiral that we've seen many, many times. He may have wanted to remove the Baku by force (Heck, I would have sent them a Quantum Torpedo), he was above killing, even going so far as to cancel the whole operation after realizing he was deceived.
If there's any movie in the Star Trek franchise that STID rips off, it was the previous movie. It covers all the same ground when it comes to what the character conflicts are and it literally ends on the same freaking note as the last movie did. STID feels less like a sequel and more like a redo.