The interesting thing about the Hope incident is, that we never actually see the ICA troops killing any civilians. They single-mindedly focus on taking out 47 and letting the civilians run away. Heck, even when Skurky fires at Travis, they pacify him by shooting him the leg and then letting him limp away. Compare that to the attack on the motel, where we saw them killing people.
My guess is the ICA/Travis was aware that it would be extremely hard to cover this up and that killing everyone in the town was impossible and would cause a very strong reaction from the US government. The original plan was probably to pretend this was a government operation against Dexter. But then the town started catching fire and they had to come up with another excuse. It was still a desperate plan that would never have worked and the fact that their troops had ICA logos on their uniforms was stupid.