A typical ban will indeed ban all account linked by credit card or battlenet account. If for some reason you wish to experiment with questionable software and want to protect your main accounts it would be wise to create the experimental account with a new copy of the game and time cards. The experimental account could then be banned and likely not affect your mains. This process would only be used for testing software or addons that have not been given a blessing by Blizz, something like the first iterations of mousecloner, or scripts produced with Innerspace from questionable sources for example. Of course using software which is known to be against the ToS or EULA is not only stupid, it is against the rules of this forum.

In no way am I condoning or promoting the use of anything that is known to be against the ToS. I also know that IS and the newer mousecloner can be used within the confines of the ToS, but it is up to the end user to guarantee their proper use.