The composure Lois has during the interview scene suggests she gave nothing up during interrogation. Contrast that against the scene were Lois is saved from the damaged escape pod and she immediately confesses to having information taken from her. Therefore, the whatever Lois may have been able to surmise about Superman's abilities, the military- at that point- does not know it through interrogating her. They do know that he can fly. They know he's alien. And they have some inkling that he has abilities to gather intel despite their attempts to secure the information (it is doubtful that Lois's location is public information). Beyond that, they don't know Superman's powers.
However, it is highly probable that there are omitted scenes or events between Superman's first contact with the military and Col. Hardy's arrival at Smallville. Why? Col. Hardy gives a short briefing, stating, "I have previously encountered and observed the beings we're about to engage at close proximity. They are extremely dangerous..."
Based solely on what we see on the film, the conclusion is possible but a stretch. Rather, it is more likely Hardy had an opportunity with Superman to observe a possible threat.