Actually altering game files usually is not allowed, due to copyright and the EULA. Me as a customer could even question this, as I cannot check these terms before I open up the package and/or install the game (meaning I cannot return the game then). You could read it beforehand on the web, but is this really required? Even if most people don't read the licences anyway?
Many people still tamper with those MPQ fuiles, not only for cracking games or something similar, but also changing some things, in a positive way. Think the "bug-hell" Gothic III at release, where fans made patches to make the game playable, as it didn't run too well on most machines. Other people don't hack for cheating, but to change the in-build hotkeys. If I'm not mistaken, those people got not banned, although Blizzard strongly advised against changing anything in those internal files, as they might be suspected (but don't want to exclude those people just for this hotkey thing, though).
The main problem lies in the fact that you probably cannot play the campaign anymore. I don't know if offline mode still will be activated or if they even banned the players using that offline mode, as you need to re-authenticate every 30 games to play offline normally (this is really BS, I have to admit - meaning the vast majority has permanent internet connection doesn't mean everyone else has).
Blizzard actually did a smart thing with that achievement system for themselves. Even if you don't care about them (it does absolutely nothing besides displaying some more or less fancy score, no purpose other than showing how much time you put into SC2), you cannot deactivate them except purposely using an in-game cheat or that offline mode, it is like killing two birds with one stone for Blizzard:
First, they provide you a reason to be online even in single player mode, and second they have something in their hands as evidence, because these achievements are obviously saved on their servers. Now you alter the game client, Warden suspects you in that thing -> ban hammer in many cases, as it seems to be you cheated to get those achievements, even this was not the main purpose of cheating the single player campaign. You can also open up the campaign maps in the editor normally, after clicking away a spoiler warning once. So maybe you just could alter the map in the editor and play it as a separate custom map four yourself, I don't know actually.
I don't want to defend Blizzard, but on the one hand it is understandable they don't allow modifying their game client. You also know they have control over your account (I know this sucks), also that you might have a deal with the devil in this respect, just for playing SC2. And as you HAVE to register it using your battle.net account first, why not staying online anyway? Plus you get those achievements, if you play the campaign normally (if you like numbers rising) ...
If that "offline mode" allowed you to play without re-authentication, it could have been better, but otherwise they probably don't want make pirating too easy - although I think those will be able to play single player without problems 
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