There's no plan at the moment to update with a patch. If we were, the plan would be to create a pak2.pak with the patch elements in it, to be overwritten when part 3 is released. We'd make that a separate download and patch the full file at the same time. But we'd really only use that option if a critical problem like a crash bug came up. So for now I guess the best thing is to distribute the sounds with your map. Otherwise it'll go from you telling us there's a bug to people playing your maps telling you there's a bug, even though it's not your fault, because they didn't get the patch.
And yeah Than, don't worry about not spotting it, I messed up too. I had a test map for the earthquakes, but I was specifying the sounds by hand, so the defaults were never tested.
Modifying entities:
There's at least one way of doing this when a map is fully compiled, without having to worry about which utility to use at which time. Get a copy of adquedit:
http://www.quaketerminus.com/tools/adquedit_v13.zip
Then open the bsp file with this program. You'll see a button to extract entities. This saves them to a text file, where you can edit them directly, add new fields, even add entirely new ents to the map. Then use adquedit to import them again. The text file is basically an ".ent" file, but the program bakes the entities into the map when you use the import function.