There's no reason to remove CFW. The bans were handed out because of the detection of illegitimate titles (FBI, freeShop, etc.). It is possible that your system has already been flagged to be banned during the next hypothetical banwave. If this happens, you will want CFW so you can unban yourself.
If you are paranoid about being banned, you can remove all illigetimate titles from your system. Assuming you haven't already been flagged to be banned, removing all illegitimate titles makes it so you have virtually no risk of being banned. Merely having B9S and Luma3DS isn't enough to get you banned.
If you are slightly less paranoid about being banned, you can just disable the Spotpass settings and the Friend List setting that send information to Nintendo and have been associated with the banwave. You could also keep your wireless disabled except when you need to use it.