Because it's really really hard to hit someone with a ballistic projectile from a distance of 20k feet in 100 mph winds (or however fast a drone flies).
I understand your sentiment, but the historical context is that this is much cleaner than previous methods.
Notice that I said in war. I'm not sure how we piece together a moral system to deal with this kind of asymmetric enemy like terrorists/rebels. War is horrible. Is this lower grade conflict any better?
If I had to take a guess, it's because 20,000 feet is too much air for a ballistic object to go through without being nudged out of its intended trajectory.
Rockets can more-or-less correct their flight path, plus it doesn't matter if they're off by an inch, a foot, or a meter.
How about chemical lasers? If you can see the target, you can hit the target.
http://www.youtube.com/watch?v=DTx_qTwQqjU
You might only get one shot out of one, but they can be quite powerful. (Considering when Real Genius was made, it's kinda prophetic. We even have a military mini shuttle around that size.)