Isn't simply not "activating" combat an active combat system? By default if someone is on your side (alignment) combat will not start(Try attacking a henchman or another player). By using this behaviour, you can remove alignments or put characters on the same alignment and throwing spells/attacking will not initiate the turn based combat we know.
For scripting, you will need to handle the "out of combat" scripts and assign them to your characters. Scripts has a heritage system so you can easily make one "base" (example : every character with X alignment attack the players on sight with their held weapon) and assign this same script to all your characters. From basic scripts you can then customize and specialize behaviours wanted for spellcasters, archers etc... (Take a look at existing scripts for examples)
I hope this helps!
