I agree with the 'theory' that the guards didn't know what was going on. After all, Ganondorf was a vassal of the king, I believe.
I'm just saying that there's no real reason for the guards to give chase, when Ganondorf was not an enemy.
We'll never really know what Ganondorf was planning. He obviously wanted the Ocarina of Time, and the Spiritual stones. Zelda left, and things in Hyrule were relatively normal, until Ganondorf started taking over while link was encased in the sacred realm. You can travel back and forth, but can't really get 'into' that 7 year timespan.
I think that the soldiers should be replaced by more competent race. Wouldn't it be cool to have gorons guarding the castle on land? If an enemy comes, all they have to do is roll at him. Maybe some Zoras could be guards in the castle moat. If an intruder comes close to the door, a Zora could sneak attack 'em. I don't quite see that happening but that would be more effective.
The soldier did do something, in OOT right before you go to the master sword you'll find a dying soldier in the back alley, so they obviously did put up resistence, they just lost and Impa used that time to escape with Zelda.