Would be cool to have a system like House or Spawnguard. Instead of "marking" out an X to X and Y to Y area, let the water settling work in your favor. Use a command to mark a specific X,Y coordinate (where to "aim" the water), then use a command to specify how many blocks tall. Then the script can spawn water in a tall column at that exact coordinate, and it'll fill the hole or whatever. More complex system could incorporate an ability to specify the width of the column to be 1, 2 or 3 blocks wide, for better fill volume for large areas.
If you know exactly how many blocks your hole is, this system would make it remarkably easy to fill even several hundred tiles worth of area, by just doing the math, and inserting columns 20-25 tiles tall at a time. The water settling would take care of the rest.
In cramped spaces, this could be problematic, but I doubt that would be an issue that arises very often.
If you're particularly brave, add another script that deletes a tile of water at a specified coordinate, and respawns that tile of water at a specified coordinate. You could create fountains that never overfill, and have endless flowing water. By making the timing of the "erase/spawn" variable, it could make waterfalls or small garden fountains. (might load down server CPUs, but worth a try).