Keep on the Shadowfell assumes players will head back to Winterhaven for their extended rests, rather than camp in the dungeon. That's not a well-founded assumption, but at least it's a good intention. Regular trips back to Winterhaven help build it up as a home base, and allow for further interactions with its anaemic residents.
The problem comes, however, from mixing the "home base" philosophy with the idea of the "living dungeon".
The "living dungeon" theory of D&D suggests that dungeons and other monster lairs are not just static environments stocked with loot-bearing fleshsacks. The dungeon residents do not rest eternally in their designated rooms, twiddling their thumbs while waiting for heroes to come and slay them. Rather, they roam naturally throughout the available space, forming a kind of ecosystem, and respond intelligently to incursions into their domain. If players enter a dungeon, and then leave and come back later, they will find the denizens waiting for them and well-prepared.
Living dungeons can be great in a campaign that's tailored for them. This kind of realism can very effectively build immersion. However, 4th Edition is not well built for it, and in Keep on the Shadowfell in particular it would be a mistake to run the game this way.
Keep is presented in the "delve format" first pioneered by Wizards of the Coast late in the lifespan of D&D 3.5. Each encounter is set out over a double-page spread in the adventure booklet, with only the largest and most important encounters getting a third page. Each room is presented as a self-contained encounter, with the monsters for that room set out in full. It's a great format for easy DMing, as everything you need for the encounter is in one place, without requiring you to access the Monster Manual or flip back and forth between multiple pages. On the downside, it means many monsters are reprinted several times in a single adventure and comparitively little space is available for descriptive and roleplaying support.
This means that encounters really are linked to the physical space in which they're intended to take place. The geography of each encounter is as integral to its setting as the creatures which populate it.
Keep recommends that if players engage the goblins on the first level of the keep and then leave without finishing the rest, when they return they'll find the remaining goblins waiting at the stairwell ready to ambush them.
This is terrible advice; you're cheating players out of the much more interesting encounters in the Torture Chamber and Chieftain's Lair, while simultaneously making them replay the Goblin Guard Room, an encounter that they've already beaten once. Plus there's a good chance that "all the goblins at once" is an encounter significantly tougher than they can handle.
4th Edition encounters are, in general, carefully balanced affairs. Moving a group of monsters from one room to another or, worse, combining them with another encounter, is tempting a total party kill, and at best will be a frustrating experience for your players.
Speaking personally, the feeling of "clearing" a dungeon, room by room, is one of the more satisfying aspects of dungeoneering. It may not be realistic, strictly speaking, but when you look at gelatinous cubes sharing space with zombies, and ghouls just down the corridor from hobgoblins, there's already a certain suspension of disbelief necessary in accepting these deadly creatures living harmoniously in close proximity. A further abstraction is a worthwhile sacrifice.
Let the dungeon stay put. Let its malevolent residents twiddle their thumbs as they wait to be slain. It may not be realistic, but - and this is what's important - it's just more fun.