We use resonant inelastic x-ray scattering (RIXS) at the Cu L$_3$ edge to measure the charge and spin excitations in the half-stuffed Cu--O planes of the cuprate antiferromagnet Ba$_2$Cu$_3$O$_4$Cl$_2$. The RIXS line shape reveals distinct contributions to the $dd$ excitations from the two structurally inequivalent Cu sites, which have different out-of-plane coordinations. The low-energy response exhibits magnetic excitations. We find a spin-wave branch whose dispersion follows the symmetry of a CuO$_2$ sublattice, similar to the case of the fully-stuffed planes of tetragonal CuO (T-CuO). Its bandwidth is closer to that of a typical cuprate material, such as Sr$_2$CuO$_2$Cl$_2$, than it is to that of T-CuO. We interpret this result as arising from the absence of the effective four-spin inter-sublattice interactions that act to reduce the bandwidth in T-CuO.