When characterizing a force as “internal” or “external” you need to be very clear what is the system. In your example you have two charges, but you also have the electromagnetic field.
If you consider the system to be only the charges themselves then the forces from the EM field are external, not internal. In this case the field does work on each charge, and the work done by the external forces on the system is non-zero.
If you consider the system to be the charges together with the associated EM field, then the forces are internal forces. No work is done on the system by the internal forces, but a non-zero amount of the system’s internal EM energy is changed to internal mechanical energy.
Paying attention to the choice of your system is critical