Yes, that's the whole idea, the individuals should be the one to decide what's valuable and what's not for them through upvoting/flagging. If the author is upvoting himself to Trending with bots, then the whole purpose of this platform is lost, but the community can still decide to flag, which is a much-needed action.
Still, I don't think that bots will ever be killed, but they can still be improved.
The bots could be killed if a superbot was created, enough delegation given to it and it began targeting all the trending/hot posts that were using vote bots. I believe Grumpycat proved this with his/her targeting that if people start losing money (in that case, bots that vote after 3.5 days) that vote buyers will modify their behavior to avoid the monetary loss.
Yes, if the people with the stick start pushing the bot owners towards change more, they would have to comply at some point.