So I created a new click bar that has two toggle buttons, one for each group.

This allows me to turn off KeyMaps for Group 1 or Group 2 - however this didn't work.
Turning off a Key Map only shuts off the front end -- the Hotkeys you are pressing. Since your Hotkeys for the most part translate to something like "send 1 to all windows", shutting off the Key Map in window 2 is irrelevant because it's only getting an instruction to press 1 in the game, which it can still do.

There is a proper solution for what you are doing, and it's to add a back end that can be disabled:

Here's a guide that will change everything you know about ISBoxer.
HOWTO: Configure ISBoxer like a pro

With this method, each character has his own interpretation of a generic idea, such as "Interrupt", and it is his own responsibility to make that translation (e.g. a DK might decide to Mind Freeze or whatever, a Shaman might use a shock, etc).

It also has an extremely simple shutoff in the form of a single Key Map that you can disable on any given character, to prevent him from doing those things (this would be the "Virtual Combat" key map in the guide).

And, there's a guy that has been working on a "complete" (all classes, specs and levels) shareable (as in you can download it and plug in your own characters with a few steps) version of this concept for WoW, with tips from me and other ISBoxer genius types. He hasn't made it available yet but when he does, I believe this is the thread to watch for it on ISBoxer.com: http://isboxer.com/forum/viewtopic.php?f=4&t=2850