yes, the dragon could do that all day... but, it doesn't seem like the actions of a powerful dragon to fight from a distance all day. However, I could certainly see it doing that once or twice.
The party psion and sorcerer both have long-range powers/spells that could hit the dragon from 400 feet, plus 40/level, or 1000 feet away. I would assume the dragon gets serious penalties at trying to drop stones from 1,200 feet up - can you even see medium sized creatures from that height?
Well, a red-tailed hawk- common to my area- can spot a mouse from 100 feet in the air, and other species will hunt their prey from 300-500 feet above and more. Among the top of the list is the peregrine, which may divebomb prey from as high as 1000 feet, reaching speeds of around 180mph while doing so.
So if a dragon has anything resembling a raptor's visual acuity, spotting targets from that height shouldn't prove to be that difficult.
As for penalties for doing so, I might vary that from draco to draco. One who loves the tactic and has the resources at hand to do so would be quite good at it. One who lives in an area devoid of suitable missiles might never even think of the tactic, so if it tried it, might be quite awful- at least as bad as using the improvised weapon rules.
Besides, its not the dragon's "Win the game" tactic to just pummel the party with rocks. Its actually a vertical version of "divide et imperium"- divide and conquer. By bombarding the party with boulders, the dragon forces the party to either seek cover or bring the fight to it (and not every 15th level PC has access to aerial travel). Close with it, and you'll be subject to its breath weapon and spells (which may be the equal of the party's spellcasters'). Close further, and you'll be in melee with it...in the air...where it can use all of its claws AND its bite AND its tail on you at will.
And don't underestimate that tail- remember the scene in the 1st
Alien movie? While transfixing one character with its toothy grin, it worked its tail around behind the target, impaling him from the rear.
In the air, a large dragon could do that
easily.
In one encounter I ran some years ago, a party on a flying ship was attacked by a HUUUUGE Blue dragon who grappled the ship from below. The party ran forward to assault the head, only to be attacked from all directions, as first one claw then another would strike from below the party's horizon. Then the tail did a massive sweep of the deck, sending many NPCs plummeting to their deaths...and almost one PC as well. He was saved by his Ring of Feather Falling, but he was effectively removed from the fight, and the party had to go looking for him later.
(BTW, the above scenario was inspired by an altercation between the 2 cats I owned at the time. One was sitting on a perch, and the other was hanging on to the perch upside down and swatting up. Sadly, yes, catnip was involved.)