Ah yes the old "nothing can ever happen because bad guy x".
The stats boosting part of the skill is quite unclear in the story, but even if it could kill the MC and so on, what would prevent the same happening to that person? The only reason MC is the only one to "figure out" how the skill works is because author bullshit, so if the story "ended" with someone not MC going OP with the skill, that would mean that author isn't focusing on MC anymore so everyone else would be free to mash two braincells together and "discover" how to use the skill on their own.
Also fearing unprovoked murder is about as pointless as fearing a meteor crashing on your head. Unless you're like, in a war zone, or a really really dark alley.
About the mastermind behind everything... So why isn't MC dead or soon to be dead? There's no point in author writing the story.
It isn't just the old "nothing can ever happen because bad guy x" when the skill is literally "instant death". It's not the same as saying that some bad guys use swords, so no good guys should ever use swords, or some bad guys use magic, so no good guys should use magic. I'm not even saying the MC shouldn't use it. I'm simply saying that there is a good reason not to train a bunch of people with it.
It is a super powerful skill, and as a result, if there are many users, the odds that some of them would try to abuse it would be very high. Look at how many powerful individuals in real life, or in most stories, are corrupt and don't care about harming others to get ahead. A couple of those in the group, and the group could die quickly. Also, your question about what would prevent others from using instant death on a user that uses it on others is why that user would then seek to eradicate all other instant death users (which supports my point). If it is used once, that also leads to why others would be afraid of it, as once it is used on you, you can't respond and they then have to be wary of any other users they don't completely trust.
Fearing unprovoked murder being as pointless as fearing a meteor crashing on your head only applies if you are teaching a lot of people how to summon meteors onto monsters' heads. I would disagree with somebody using preemptive instant death against other users, just because of being afraid they might use it on them, but there are overly cautious types, and if one of them had seen people betrayed by companions in the past, they might fear that in the future, and act to prevent that.
I actually think it more likely that there isn't a mastermind, by the way. There didn't seem to be any indication of reporting it. I just said the problems with training a bunch of users "would be a great reason" not that it was the reason it is called a trash skill. If there was a powerful user in the past, I think the more likely scenario would be that he is already dead (either of old age, or because of being taken down by a bunch of heroes), and the treating it like a trash skill is a remnant from preventative measures to cover it up. If heroes are monitoring it, they may still not want to kill potentially innocent users, and thus just try to prevent them from adventuring by calling it trash.
Another possibility I didn't mention before, is that he only managed to unlock its strengths because of getting so many points from a powerful monster, and that almost everybody else that still tried to adventure would try to use it from a distance and keep failing, or on weak opponents up close and get killed before they got enough skill points to get stats and get stronger because they didn't have enough defense. It just seems at least a couple others would have lucked into it like he did at some point, and gotten stronger, so then the question of why it is considered trash makes a cover-up a decent possibility.
(It could be the author didn't think too much about it, though, and just picked a cool skill and decided in this world it is trash, because that is a popular version of fantasy, now.)