And why weren't the Marines allowed to engage the snipers? They were shooting first and the Marines clearly had a right to defend themselves.
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In the beginning the snipers were firing at the marines as they were taking positions around the embassy. The marines should have been allowed to shoot back at the ones who were firing at them.
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The short answer is simply that nothing in the rooftop scene made any sense, and that the plot of the movie was a weak contrivance that depended on the idea of some big bad Americans blowing apart a bunch of little kids throwing rocks.
Several shots showed that the snipers were on the roofs of the other buildings in the area. When the colonel said, "Engage hostile targets as they appear," the captain said, "I have women and children in my line of sight." However, the women and children would have had to be magically suspended in the air between the roofs of the buildings in order for that to be true. How could the crowd of demonstrators been in the line of sight? They were on the ground, and we could see that they didn't have any weapons besides the rocks and pieces of masonry they were throwing. They couldn't have done anything to the Marines on the roof even if they did have rifles, since they were on the ground and the Marines were on top of the roof and behind parapets. Anyone who was capable of hurting the Marines on the roof would clearly have had to have been situated at least as high or higher than the Marines on the roof.
When the colonel asked the captain what it was that he didn't understand about his order, the captain -- whom I can only suppose was profoundly mentally retarded to ask such a question -- replied with, "Are you telling me to fire into the crowd?" When the Marines (bafflingly) direct their fire downward into the crowd of demonstrators, you can actually see them ignoring the rooftops across the yard from them (some of the same rooftops where we could see snipers shooting from in previous shots) in order to do so.
It's a stupid scene, and -- honestly -- kind of a stupid movie to build the entire progression of the plot around it. The movie is only saved and made somewhat entertaining by the acting talent of Samuel L. Jackson, Tommy Lee Jones and Guy Pearce.