Funny, but OTOH:
"Kirk fails to protect his crew... and the Enterprise... and downtown San Francisco"
That clip is true to the movie, and that's a problem IMHO with movies nowadays. Nobody matters as long as they kill the bad guy (ok, they didn't kill Khan, but that was just becasue they wanted his BLOOD! How taking BLOOD by force can be a good guys thing?).
In the previous movie, Kirk ordered to open fire against a enemy already defeated and in his knees (figuratively, it was a black hole).
Other moveis are examples of this trend. I was unconfortable during Transformers 2 seeing childhood hero Optimus Prime executed a defeated enemy with a shot in the face.
Enemies during the 80's, for example Indiana Jones', always died by their own evil actions. This is different.