We have studied the anisotropy in the in-plane resistivity and the electronic structure of isovalent Ru-substituted BaFe$_2$As$_2$ in the antiferromagnetic-orthorhombic phase using well-annealed crystals. The anisotropy in the residual resistivity component increases in proportional to the Ru dopant concentration, as in the case of Co-doped compounds. On the other hand, both the residual resistivity and the resistivity anisotropy induced by isovalent Ru substitution is found to be one order of magnitude smaller than those induced by heterovalent Co substitution. Combined with angle-resolved photoemission spectroscopy results, which show almost the same anisotropic band structure both for the parent and Ru-substituted compounds, we confirm the scenario that the anisotropy in the residual resistivity arises from anisotropic impurity scattering in the magneto-structurally ordered phase rather than directly from the anisotropic band structure of that phase.