Sure if the federation doesn't mind possibly alienating any potential allies for their war after the klingons made it know the federation destroyes civilizations that don't exceed to their demands.
Plus again the federation likely wanted to use the planet as a base for the war. Kind of hard to do if you burn it to a cinder.
Kirk's orders were quite clear. He wasn't there to allow the Federation to set up a base of their own or to convince the Organians to ally with the Federation. in his own words:
Kirk - We are to proceed to Organia and take whatever steps are necessary to prevent the Klingons from using it as a base.
The Federation was expecting war to break out at any time and sought to prevent the Klingon advance. Sometimes in war the civilians suffer for "the greater good". See Hiroshima & Nagasaki, two cities with no military value but chosen to demonstrate the power of the atomic bomb. Perhaps the most appropriate modern comparison would be the Dresden Firebombing. A strategic location that was attacked without regard to the civilian casualties.
The historian Alexander McKee has cast doubt on the meaningfulness of the list of targets mentioned in 1953 USAAF report and point out that the military barracks listed as a target were a long way out of town and not in fact targeted during the raid.[126] The 'hutted camps' mentioned in the report as military targets were also not military but were provided for refugees.[126] It is also pointed out that the important Autobahn bridge to the west of the city was not targeted or attacked and that no railway stations were on the British target maps, nor were the bridges, such as the railway bridge spanning the Elbe River.[127] Commenting on this Alexander McKee stated that: "The standard whitewash gambit, both British and American, is to mention that Dresden contained targets X, Y and Z, and to let the innocent reader assume that these targets were attacked, whereas in fact the bombing plan totally omitted them and thus, except for one or two mere accidents, they escaped"[128] McKee further asserts, "The bomber commanders were not really interested in any purely military or economic targets, which was just as well, for they knew very little about Dresden; the RAF even lacked proper maps of the city. What they were looking for was a big built up area which they could burn, and that Dresden possessed in full measure"[129]
http://en.wikipedia.org/wiki/Bombing_of_Dresden_in_World_War_II#That_the_bombing_was_necessary_or_justified