You'll need two charge controllers for the two fractions of the panels.
Separately charging or loading voltage-wise fractions of a battery risks getting the upper and lower parts to different states of charge. Then when your load exceeds your charging you can drain the lesser-charged section and drive it to reverse polarity (with major damage to it) because of current driven through it by the still-charged fraction. On a per-cell basis this is what doing an equalizing charge is intended to prevent. You'd be creating the situation deliberately.
There are three-terminal devices - essentially switching regulator/voltage converters - to pull power from the more charged part and drive it into the less charged part (with some loss). You'd be way ahead to reconfigure the panels for 48 and get a new controller.
But you said your load was at 24. That's not good. (Your balancer would have to handle the whole charging current of the 48V stack - half the total power.) Can you reconfigure the load for 48?