The ones that carried out the attacks are all dead, so it's rather difficult to put them on trial. The others don't have to be put in a civilian trial, they can be dealt with by military tribunal and if I'm not mistaken, there is no requirement for the military tribunal to be public in the same sense that a civilian court is public.
What you are ignoring, is the fact that these terrorists that are being held consider themselves soldiers in a jihad. They do not fight for a nation state, they fight for the jihad. Since they don't fight for a nation state, they are not protected by any article of the GC except article 3. Note the part I bolded does not specify civilian or military courts. Also note that the bolded part is a protection, not a requirement for a trial.
Article 3 of the Geneva Convention.
In the case of armed conflict not of an international character occurring in the territory of one of the High Contracting Parties, each Party to the conflict shall be bound to apply, as a minimum, the following provisions:
(1) Persons taking no active part in the hostilities, including members of armed forces who have laid down their arms and those placed ' hors de combat ' by sickness, wounds, detention, or any other cause, shall in all circumstances be treated humanely, without any adverse distinction founded on race, colour, religion or faith, sex, birth or wealth, or any other similar criteria.
To this end, the following acts are and shall remain prohibited at any time and in any place whatsoever with respect to the above-mentioned persons:
(a) violence to life and person, in particular murder of all kinds, mutilation, cruel treatment and torture;
(b) taking of hostages;
(c) outrages upon personal dignity, in particular humiliating and degrading treatment;
(d) the passing of sentences and the carrying out of executions without previous judgment pronounced by a regularly constituted court, affording all the judicial guarantees which are recognized as indispensable by civilized peoples.
(2) The wounded and sick shall be collected and cared for.
An impartial humanitarian body, such as the International Committee of the Red Cross, may offer its services to the Parties to the conflict.
The Parties to the conflict should further endeavour to bring into force, by means of special agreements, all or part of the other provisions of the present Convention.
The application of the preceding provisions shall not affect the legal status of the Parties to the conflict.