It is highly improbable that the G.I. in his encounter with the Doctor at Trenzalore asked the question outlined in the prophecy. The G.I. who was only interested in the Doctor's name will not figure in the events that transpire at Trenzalore in the forthcoming Time of the Doctor special (although he might influence things somehow without being a player in the events) which will be centred on a struggle between the Doctor and his enemies. That is significant because the prophecy appears to refer to events that happen on the fields of battle. The Time of the Doctor special rather than the Name of the Doctor episode would seem therefore to present the characteristics of time, place and situation that are in keeping with the details of the prophecy.
Furthermore, the lines from the prophecy "when no living creature can speak falsely or fail to answer" do make it hard to accept that the situation presented in the Name of the Doctor episode corresponds to the one mentioned in the prophecy. The Doctor did resist answering (and did not answer) despite being in a situation of extreme duress.
There are some grounds to suppose that the question also is really more about the Doctor's identity or self-knowledge than simply his name because we know, based on another comment from Dorium, that the Doctor has been running from this question all of his life. The G.I., in the Name of the Doctor episode, wasn't concerned with this aspect which arguably is essential to the prophecy.
The terms of the prophecy were not fulfilled, in my view.