The best approach might be to use a smoothing method that can handle non-manifold edges. SurfaceNets, and the more recent Multi-label SurfaceNets (Frisken, "SurfaceNets for Multi-Label Segmentations with Preservation of Sharp Boundaries", J. Comp. Graphics Techniques, 2022) was designed to handle surfaces where edges can join more than two faces. (This happens frequently in multi-label volumes where such edges often occur where two materials join). The smoothing algorithm described in the paper can handle those cases. It can also preserve sharp edges and corners and minimize self-intersections. The paper has a link to C++ code. Note that as of this writing, the vtk implementation does not use the SurfaceNets smoothing method.