If things weren't Quest-locked, then it would be almost impossible to explore without breaking a quest... any quest. Then I can only imagine the level of butt-hurt crying about how only five quests in the game can be completed...
The way it is now is clean, orderly, and saves the continuity of most every Quest-line in the game. Having places and items quest-locked is not only necessary, but is also beautifully done in The Elder Scrolls series.
Actually, quest-locked dungeons are
not necessary; rather, what's necessary is that they design the quests so that they don't break if you explore a related interior and/or pick up a related item therein. Do that, and you remove the complaints of both groups at once since neither situation occurs.
There's already a partial example of this in the game: inside the final zone of Hag's End (that has the same name) is a false wall that is tied to a Dark Brotherhood quest. You can go there any time you want, since the location itself isn't quest-locked, however the chain for the false wall only appears if you're doing the aforementioned DB quest. Granted the 'magically concealed trigger' is a rather tired device, but it's a lot less invasive than having the entire interior arbitrarily sealed off.
Alternatively, have the quest-related portion of a given ruin be separate from the rest. Labyrinthian already does this with a side-chamber near the main door, however it has the problem that the seal is on the inner door rather than the outer one, which leaves only a small and seemingly pointless (as it's empty save for a couple of 'junk' items) vestibule accessible. In fact, you won't know said door
is quest-related until you're actually on said quest, which is a bit obscure in its own right, since it gives the standard 'sealed from the other side' message that implies it's an alternative exit from the main dungeon. Which it isn't, since they're not physically connected in any way.
They could also borrow a page from the way player houses work: have quest items/NPCs start initially disabled, and then enable then when the relevant stage of the related quest is activated. That way it's literally impossible to break the quest, since the thing that would cause said breakage only exists for a given character when needed.
Oh, one other thing:
DO NOT have quest stage advancement tied to body count, unless you're going to provide all the relevant bodies when necessary. The CW fort sieges do this more or less correctly, but a certain quest in Riften
definitely does not, which causes unnecessary glitches and headaches.