It's also worth reading the newer studies regarding genetics, like
this one which states that "The branch of the canine family tree that includes domestic dogs diverged from that of the gray wolf more than 15,000 years ago."
You can't domesticate SOME aspects of instinct (especially not those which are related to basic survival or the basic nature of the type of species: all prey animals have very basic instincts in common, as do all predators), but you can certainly breed selectively to minimize or maximize those instincts. And horses absolutely CAN be bred and trained away from those instincts, otherwise you'd never be able to trailer or stable them (although many people forget that horses are naturally worried about dark, enclosed spaces like trailers, and don't bother actually training the horse to accept trailering)!