I think disabling-enabling scripts themselves will not work, esp. if the CBS doesn't modify Scene_Battle class (i.e. writing its own battle scene), although I believe most ABS modifies that class.
I am thinking something like this:
1. Have as many CBS as you want, leaving the DBS as it is (if used).
2. Make sure all CBS doesn't modify Scene_Battle class. If it is, change the CBS' Scene_Battle class name to something else.
3. Either:
a. Define an in-game variable that will determine the battle system you'll be using, changing its value using Variable Processing event.
b. Define a script variable, with the same usage as (a), and modify its value via Call Script event.
4. Change the Interpreter a little bit so we can still use Battle Processing event. By looking the value of the variable in (3), choose the appropriate battle system and execute it.
I might be wrong though (didn't test it)...