I am unclear as to why there would be any "rewriting" of code. Sure there would be new code written, but why would old code need to be rewritten?
It seems to me that if the devs were seriously interested in adding some control (not going into specifics) for battles they would likely approach it as an additional module to the existing game (think Breach for those that know Breach and what it wanted to be).
With a set up like that if a player (since this is limited to SP only, or hot seat I suppose) wanted to not use this module he would not use it (selected at start up, or at every battle ala AoW). I have given alot of thought to how combat could be made more user controlled, and I've come to the conclusion that it doesn't need to be, mostly because I see this as another way that people will just ***** about the AI, but also because it really wouldn't add that much to the game, and could likely detract from the game.
As always to each their own, the more that is discussed the more we will all learn (usually...

)
Here's a final thought though, if it were possible for third parties to make the combat module (kinda like the combat simulator I suppose) then I think most everyone would be happy. I'm not sure if that's really possible though.