Even Milton knows the brain has to be destroyed to "kill" walkers. Though you would think the fire would be enough to thoroughly cook the brain, thus destroying it.
I seem to recall somewhere that Kirkman said if the burned hot and long enough to destroy the brain that fire would work. But I could be wrong.
In any event, Milton (or whomever) was probably trying to incapacitate the maximum number of walkers in the shortest amount of time. After all, it isn't like he could just go in and start firing off head shots without alerting people and he's hardly a Michonne or even Andrea when it comes to being stabbing them in the head.