Every case is fact specific but if you follow your logic through to conclusion you get an unarmed black kid shot dead walking through a gated community.
If that unarmed black kid is positively identified as a time traveler who recently destroyed an entire planet with a weapon of mass destruction and has been VERY clear about his intention to do so again given half the chance, then your analogy makes sense.
To be less hyberbolic: if the unarmed black kid is someone known to have killed someone AT ALL and is very clear on his intention to do so again, then your analogy makes sense.
I think the kid was pretty much minding his own business and got a bit lippy when he was challenged.
The point is that positively identifying someone as a threat can often be subjective and proven wrong in the cold light of day.
"Positively identified as a criminal" =/= "Subjective prejudicial judgement based on a hunch"
It's not like Kirk shot the Narada to pieces just because the Romulans killed his father. Nero committed some very specific actions that lead to the deaths of billions of people and circumstances suggest an extremely high probability that he would do so again. For everyone's safety, he needs to be neutralized. Captured if possible, killed if necessary.
The kill became necessary in Nero's refusal to surrender. Even the slim chance that he and his crew might survive the destruction of their ship and remain free to act is, simply, unacceptable.
If you want to get more imaginative with the tech, then as soon as your enemies' shields are down, you beam across neutralising gas. Then you beam them off. If their shields are still up, they're still a threat.
We get blinded by the sort of "pulled from my ass and it worked the first time" tech progression of Star Trek, but in the real world alot of those kinds of elaborate stunts we envision Treknology being capable of would require a fair amount of prototyping, testing and simulation, training and practice, in order to be used successfully.
It's not the kind of thing you can pull off in a flash of inspiration and say "Hey, Scotty, you think you can rig up a dose of knock-out gas, beam it to strategic positions within the enemy ship -- in just the right distribution to make sure it gets anyone, but not dense enough to cause respiratory problems -- and then quickly target and beam aboard all of the Romulan life forms there, six at a time, making absolutely sure you don't accidentally beam over someone who is still conscious?"
The problem with Treknology is that using it properly would suck the fun out of the fights so we have to pretend like it can't do it.
No, the problem with Treknology is that TNG+ treats as if it were sorcery and not science: that you can conjure up just about any working gadget with the proper incantation of science-sounding words.
Engineers are hardly above having to improvise to make ends meet, but they go through a process of trial and error, experimentation, troubleshooting, testing again, retrying, more troubleshooting, etc. Even Apollo 13's famous air-scrubber improvisation took several hours of hard work by some of the best engineers on the planet; the one thing they DIDN'T do was sit in a room somewhere and have someone say "What if we modified the S-band radar to emit a forced neutrino pulse that will convert the Carbon dioxide into carbon and oxygen?"
