Well, I'll give you this one. The five minute rest is a new 4e conceit that I don't really use.
My PCs rest for all of 30 seconds and that's if it take that long to reach the next encounter.
Basically, once the hectic fight is over, they check temselves for wounds, take a deep breath (and regain encounter powers!) and then resume hunting the monsters. If they haven't successfully killed everyone before they could sound the alarm, they run into monsters in the next room and the twenty seconds delay since the end of the previous fight barely explains why they had the time to grab a weapon and gather in a more sensible formation.
A four encounter dungeon like, say, the Room of Eyes in the Thunderspire labyrinth would probably be cleaned out in about three minutes to four minutes of real world time.
Imagine a bunch of commandos sweeping a terrorists hide out.
I don't know that particular dungeon, but I imagine if the alarm gets sounded immediately when the PCs attack at encounter 1, encounters 3 and 4 will have time to group themselves together. In a five encounter dungeon, that at least encounters 4 and 5 will manage to group themselves together after an initial alarm seems even more likely. Of course, as GM you could use a 4 encounter dungeon rationalized as "the last encounter is the hardest because two groups of monsters were able to band together in the chieftain's room."
If you essentially assume that a short rest takes 0 time but can't be used in combat, and that monsters try to gather themselves into larger groups to fight the PCs if given sufficient time, then PCs will start sweeping through dungeons killing everything as quickly as they possibly can.
This has some consequences for their ability to find stuff as they go along (and disarm traps or the like), and makes "per encounter" and "spending healing surges after the encounter" an even stranger concept, but those are just game concepts, not simulationist ones, anyway.