I'm no expert so there, but my guess would be that it does not matter much if the 24V comes from a solar system or a battery system as long as the controller can handle the voltage and current (although it could possibly throw an MPPT one through some conniptions if can't do its optimization bit?). However, the charge controller is built to charge a battery, with all the functions and constraints thereof, not to deliver 12V to some random circuit, I would think. Without the battery things may well go out of wack. But experts to the rescue!
It's unclear to me what you are trying to do but if you have a 24V battery system and you need 12V, aren't there some devices specifically built for that?