There are two major problems with your reasoning here:
- There is no meaning to the absolute value of the energy in classical MD potentials. It can be shifted arbitrarily without any impact on the simulation. Thus you cannot infer anything from it. If you want to know if something is attractive or repulsive, you have to look at the gradient, i.e. the force or at energy differences.
- There is no “background” charge applied. Rather, if you have a system that is not neutral, you would have a diverging term in the lattice sum at the gamma point. Or put differently, the energy of the periodically replicated system would be infinite. That term is simply discarded which in turn means that it has the same effect on the potential as if the system was uniformly shifted to be neutral, but there is no explicitly term added for that (and if it would it would be infinitely large).