The idea of a massive attack is good, gives the PCs something to do whilst Elminster chucks multiple world-shaking spells. My advice mirrors the "deus ex machina" camp in that it's not really necessary to roll the damage from Meteor Swarms, or make the DC 35 saves from Dragonbreath. Keep your players involved in their own struggles.
One possible scene that could transpire would be El blasting a Colossal-sized red dragon with a nasty spell, killing it mid-flight. Now several tons of dragonmeat comes crashing down nearby, possibly at terminal velocity. Before they know it, the players would find themselves in the middle of an inferno from which they have to escape, and/or save less fortunate souls.
Instead of killing Elminster, I strongly reccomend leaving nothing "writ in stone" so to speak. If Elminster is missing/presumed dead, there are a lot of powerful, heroic folks wandering the Realms who would make recovering Elminster their top priority. Which provides you, as DM with lots of opportunity. Instead of removing just one CR 39 wizard from Shadowdale, you have effectively tied up most of the Epic level heroes, and nearly every other good-aligned person of above 16th level in a mass search and rescue mission.
Leaving the forces of EVIL a window of opportunity to engage in all sorts of mischief. Why, only the bravest of a new generation of heroes could possibly oppose such a crisis!
All in all, it sounds like a pretty solid idea for a campaign. Heck, there is even room for a follow-up campaign when Elminster and Company return from parts unknown, and find all of these upstart heroes who think they can save the realms better than the Old School.
