Not all third-party programs are hacks.
Skilled Starcraft players used to use 3rd party programs such as PenguinPlug to have enhanced features such as first-person replays, showing you specifically what the player saw on his screen, what units he selected and what orders he gave them, or auto-replay saving, or in-game APM measurement, or a warning when you weren't spending as much money as you should be, or if you were getting close to your supply cap and should start spawning more overlords before your army actually NEEDS more overlords (because it will later.)
Or they'd use Hamachi or iCCup or PGT servers instead of Battle.net servers.
Ironically enough, Blizzard proves that they DON'T care by releasing a patch that stops these types of programs from working. Then their patch fixes 2 minor issues and adds in ~25% of the features that the third party programs had, and people need to start coding again.
If the game was designed well in the first place, or had the effort put into it, two guys with free time shouldn't need to design a program to allow Broodwar to load in a window. It should just have a windowed mode that Blizz created with their money silos that they're too busy swimming in to fix latency issues or add features that the player-base had been asking for.
Unfortunately, Blizzard just bans you for using things like this.
Now, on the other hand, maphacks are understandably bad, or mineralhacks or speedhacks and such.
But a program that just takes information that the game already knows and that the player already knows and makes it easier to notice, comprehend, and understand? That isn't cheating.
If it was, Blizzard wouldn't allow UI addons like Arena Unit Frames, ForteXorcist, and DBM. In fact, they wouldn't allow any UI modification in WoW, or macro scripting, or G15 keyboards.
The truth of the matter is that they try to let something like Starcraft grow due to player creativity - UMS maps, melee maps, a full-fledged map editor, etc... But then players need to create their OWN map editor like SCMDraft or StarForge in order to do these things. If someone mods their game, they can still play it on battle.net, but only with other plays with those same mods.
If someone creates a third-party program to help them learn (BW Chart, say) or a channel chat room moderation bot, it's apparently a terrible terrible thing. And I don't like the double standard.
That said, if all 320,000 were hackers, I'd be pleased with this ban. But I get the feeling most of them were just average people like you and me who found out a way to have more fun without overshadowing other players or competing with them in an incorrect fashion - wallclimbing, perhaps, or rocket boots + parachute cloak to get from lumber mill to gold mine?
When all is said and done, I personally don't violate the terms of service and wasn't affected by this ban, but I'm sure some of my old friends who still play Starcraft in a somewhat competitive fashion were banned for all the wrong reasons.