More than 1 way to protect our planet.
Yes, there are plenty of potential ways to protect us. A missile is not a good choice. Now, if we can hit the sucker far enough out to give it a nudge, that's the answer. We can't blast it away, but we might be able to redirect it.
Landing some type of thruster on it sounds great for a movie, but in reality, would be rather complex. Just slamming something with enough mass and speed into it might alter the trajectory.
but there's the rub.... We have done a good job at mapping out local bodies in space, we can do a lot of calculations as to orbits and such, but we really have no clue what will happen if we alter it's course, so many things out there can alter it's course, we could redirect it, make it miss, then send some massive pile of rocks out of the ort cloud at us.
anyways, a plan that's not even at the planning stage + government = nothing done in a timely manner. In fact, we'd be best off to crowd source it, and allow private industry to save us, they'd probably actually get it done.
Right now, we know where apophis is, where it's heading, and once it passes in a few years, where it will be next pass. Any nudge in any direction alters all of that, and we're back to guessing.