Intentions are irrelevant here. He could be the nicest person in town and I'd still kill him.
A man who can control the minds of government and military officials, start an atomic war, and wipe out humanity before lunch simply cannot be allowed to live. What if he evolved and gained the ability to mind control even REALLY strong superhumans?
It's just too much of a risk to let him live...
To be fair, the world of Superhuman has gone well beyond the point where nuclear warfare is an actual threat. Jake couldn't have done jack with those nukes, unless I'm guessing they were launched somewhere in-sector or he had permission from someone in another sector not to have them intercepted. The MC theorises he was going to use them on Ella, for all the good it'd have done him. We've seen from her performance at the Battle of Diamonds that she'd have walked off a nuke like it wasn't even there. The explosion wouldn't have done anything and the radiation probably would have just been annoying to her at her level of mastery over her Body trait. Would it have been bad, yes. Would it have ended humanity? He couldn't even if he wanted to, and if the MC who's canonically a bit of a dumbass knows that then so does he. And that's assuming he'd even have the will to drop a nuke in a populated area or anywhere near himself.
And unless Jake's hitting without outside assistance level 5 and finds a way to massively amplify his rate of power growth, he couldn't pull off mind control of stronger Superhumans. Subtle suggestions for things you were already doing will work on higher levels, direct commands that conflict with your desires not so much, as shown when he tried to order the MC only for his superior amounts of power to cause him to no-sell his control and when it was pointed out to Lexi that the tour wasn't supposed to go to to restricted areas. The man would have been wiped out before he even knew what happened if someone like Malik or Bernhardt cared enough about him to do it, let alone someone like Zack or Deus.
Granted, he had a shot at being the most busted thing on the planet and to manifest a power called Order at one point according to Aglaecwif, with Ella noting he'd inherited both Authority and Power, but had only manifested Authority due to him being soft and weak-willed in comparison to the MC. Mindset is important, and Jake's just not a natural killer. He became a lesser threat and will probably never again be on an actual fully manifested dual trait user like the MC's level as soon as he partially botched his second evolution. Even at level 2, he couldn't hold the level 1 Deryl under his control for too long.
I'd still have killed him just for the Amber and Liz thing, let alone the Jess thing, but considering Deryl is a friend of the MC's despite everything in their past, present and future you can absolutely forgive and spare Jake should you feel like it without it being seen as out of character. The MC seems to be more of a Chaotic Neutral type by default, not particularly caring about traditional morality and just doing what he feels like, even if he's pure and moral it doesn't stop him from dealing with budding supervillainess Tiffany or always canonically at least befriending the bloodthirsty criminal duo of Michael and Alice.
The world likes to run in circles it seems. At least it means the game isn't losing viewership anytime soon since this argument's revival usually means new people have come along.
