Wolverine wasn't consistent about this, in another comic he was supportive of Spider-Otto becoming brutal lol.
At least the plot armor here is far weaker than the Slott written issues, in which characters only think "Something's up... Oh well" lol.
Also worth keeping in mind Otto trying to kill most of the planet was written by Slott himself too, for whatever reason Otto's attempt at being good in Superio is supposed to be taken seriously, when about 10 issues before he tried to kill the planet, and he starts Superior seemingly killing Spidey, yeah...That said, if Rachel had mind-scanned him, anyway . . . well, I'd think uncovering Otto Octavius lurking as the dominant consciousness in Peter Parker's body would be a slightly bigger deal than Rachel violating the sanctity of his psychic boundaries, given that Spider-Man was an Avenger in (relatively) good standing at the time and Otto could have easily used that to gain access to technology, weapons, and/or other resources possessed by the Avengers that he could then turn into something much more dangerous to the world at large. That, and "Superior Spider-Man" was him coming off a scheme to make sure his name would be remembered forever --- as the greatest monster that ever lived --- by burning the planet to a cinder and taking almost everyone on it (99.92% of the population) with him.
Yes, I'm still a tad bitter after nearly a decade.