* Spock wipes Kirk's memory of Rayna to save him the pain. That serves no purpose. And come STV we find out that Kirk never wants he pain taken away.
* Spock forces his katra on McCoy. An act that cause side effects that gets McCoy arrested and facing a life time in a mental hospital. And if Kirk hadn't recovered Spock's body? Sorry Bones, see you on visiting day.
* Spock forcibly restrains a struggling Valeris who was refusing to answer questions. at the time there were fans that raged that that scene was (basically) a rape scene played out in front of the main characters with Kirk demanding information as she screamed out.
Rayna was probably one of those humanoids who Kirk thought was 'the one', so it's a clear case of Spock believing his intentions are right but not really thinking through what would be best for his friend.
But I do agree with your assessment of Spock mind melding with McCoy and the damage done to McCoy. The way I see it's a case of character assassination upon poor old Spock! That was a bad idea period, but sadly a necessary evil to get Kirk and the crew back to the genesis planet.
As for the third case there were some high stakes involved. Chancellor Gorkon was assassinated and a new war looked possible. Lives were on the line and Spock, angry by Valeris' betrayal, forcibly assaults her mind to find out the perpetrators. But that's the point, in that situation it's a case of the needs of the many outweigh the needs of the few, or the one. It's a DS9 moment of sorts but I like that, I appreciate that controversial aspect because it serves a point. That's Star Trek at its finest IMO.
Likewise in STID a little character assassination happens to Spock when he performed that mind meld on Pike. It was stupid, immoral and reckless and cheesed me off in the same manner as Prime Spock transferring his katra to McCoy. What were you thinking Spock?
Every series has had moments of character assassination or instances which totally destroy a character's credibility. But I'm a forgiving sort and that's why I rather enjoyed Nu Spock talking about his emotions with Uhura, despite him mentioning his mind meld with Pike- which was a douche thing to do. It's an annoying thing but there is a decent payoff halfway through the movie.
But don't worry the JJ Trek films don't even come close to the biggest character assassination of them all; Sisko poisoning the atmosphere of those Maquis worlds. To this day I still have not forgiven the episode 'For the Uniform' for having Sisko do this.
Lastly over the years we have all mapped out the flaws, faults and down right stupid moments of all the Star Trek series (and films). So let's also map out the flaws of STID. Orci and Kurtzmen tried to address problems (revealed by fans) of Star Trek 09 and correct them in STID. If we know where STID went wrong in places then that could be vital feedback for the writers of the third Nu Trek film. Let's not shy away from STID's blemishes, that's what I'm saying.
And though I was disappointed with STID I am still hopeful that the third film will be a lot better. So this is not trolling, this is constructive criticism and one little piece in the bigger picture of understanding STID.