We have examined the properties of exfoliated and restacked MoS2-malachite green (MG) inclusion compounds to provide insight into the MG-MoS2 interactions that characterize these materials. The results of X-ray diffraction experiments indicate that MG included into the restacked structure adopts a flat orientation approximately parallel to the MoS2 sheets. Second-harmonic generation experiments conducted on the exfoliated and restacked materials provide information regarding the averaged orientation of the MG. At low MG coverage, our results support the X-ray diffraction findings, and yield large averaged orientation angles, consistent with a flat orientation of MG between the MoS2 layers. However, as the MG coverage is increased, the SHG results indicate averaged MG orientations that are much more upright, consistent with the expulsion of excess MG from the layers to the outside of the restacked crystallites. Together with X-ray diffraction and adsorption isotherm data, our SHG results provide a model for the exfoliation, adsorption, and subsequent restacking of these MG-based inclusion materials and demonstrate the utility of nonlinear optical techniques as probes of these interesting layered structures.