So according to you, this "genius" didn't set up the kill switch in a way that he has the final say on whether or not it activates.
He wouldn't have been the one to set up York's hypothetical kill switch you melt
nor a way to simply put his Satelittes on stand by like the computers they are to prevent that?
York is not a robot. Robots don't poop. She's a clone. And Vegapunk's sentiments about the humanity and free will of Stussy explain why he gave the same to York.
As for the Seraphim, if that was a legit worry of Vegapunk, he could simply send them somewhere long enough to execute whatever they need to do to get rid of the betrayer.
The minute he sends the Seraphim away, he's alerting York that something is wrong. She calls the Gorosei, and he's finished.
He could also wait until she's unconscious by sleeping or napping as we've seen orders by those with higher authority being overwritten by those with lower authority if said higher priority figure is ko'd, and that's assuming that the Seraphim were ordered by York to protect her in the 1st place.
Her authority just comes back into effect once she wakes up, and they can't override a previous order of the same level.
If Vegapunk isn't expecting York to have orders given to the Seraphim to protect her, then that still doesn't excuse his inaction as there isn't really anything preventing him from doing so. But thanks to his inaction, York can now build a Mother Flame for the World Government to use against innocent people to nuke any island they desire to be rid of.
The Mother Flame already existed, and he believes in its existence regardless due to the possibility of free energy. It's the classic Oppenheimer dilemma.
What's preventing him from doing something to York is that he needs to warn the world once the effects of Lulusia are felt, and he has no way of guaranteeing that if he attacks York. He wipes his memory to keep that plan secret until after that happens.