There really isn't any reason that a break has to be 5 minutes.
Your party has made it through the gauntlet, having dispatched the hobgoblins in your way, and are now out of sight of the hobgoblin bowmen on the ramparts. As you round the corner you see a hastily assembled barricade in front of the doors to the inner keep, and the hobgoblins behind it have a mix of long spears and crossbows. However, it is the sight of a hobgoblin taskmaster whipping several slaves as he directs them to reposition a pair of light ballistas to point in your direction that makes your survival instincts surge, this battle is far from over and you draw on your reserves to see it through. You steel yourselves for the coming fight, spend healing surges and refresh encounter powers as though you had taken a short rest.
As per a game balance point of view, the gauntlet the players just made their way through was designed to challenge them under the assumption that it was a full encounter (maybe even a very difficult encounter at that), and the barricade is designed to be a very difficult encounter. 4E is designed such that the mechanics just assume that a short rest would be given. However, story wise, it doesn't make any sense to stop for 5 minutes after passing through the gauntlet, however mechanically the players are not making any sort of risk vs reward choice to rest or not to rest. So I think the reasonable conclusion is to just pretty much say "beating the gauntlet was a milestone, you get the effect of a 'short rest', even if you don't actually have 5 minutes. Seeing a pair of ballista pointed at you focuses the mind and all that."
Now, if they had defeated the keep lord, and he runs off down a secret escape passage with a sack of gold, well, you give the players the choice of regrouping (taking a rest) or following in hot persuit (not taking a rest).