We make simulated version of all humans and put them in cyberspace. At that point we proceed to kill all people.

At the very lesat, by this point we've killed a lot of people. the fact that they've been backed up doesn't make the murder less henious.

Whether or not 'humanity' gets destroyed in this scenario depends on the definition that you aply to the word 'humanity'. If you mean the flesh and blood, the meat and bone, then yes, it gets destroyed. If you mean values and opinions, thoughts and dreams, then some of them are destroyed but not all of them - the cyberspace backup still have those things (presuming that they're actually working cyberspace backups).