The saddle point approximation of the path integral partition functions is an important way of deriving the thermodynamical properties of black holes. However, there are certain black hole models and some mathematically analog mechanical models for which this method cannot be applied directly. This is due to the fact that their action evaluated on a classical solution is not finite and its first variation does not vanish for all consistent boundary conditions. These problems can be dealt with by adding a counterterm to the classical action, which is a solution of the corresponding Hamilton-Jacobi equation.In this work we study the effects of polymer quantization on a mechanical model presenting the aforementioned difficulties and contrast it with the above counterterm method. This type of quantization for mechanical models is motivated by the loop quantization of gravity which is known to play a role in the thermodynamics of black hole systems.The model we consider is a nonrelativistic particle in an inverse square potential, and analyze two polarizations of the polymer quantization in which either the position or the momentum is discrete. In the former case, Thiemann's regularization is applied to represent the inverse power potential but we still need to incorporate the Hamilton-Jacobi counterterm which is now modified by polymer corrections. In the latter, momentum discrete case however, such regularization could not be implemented. Yet, remarkably, owing to the fact that the position is bounded, we do not need a Hamilton-Jacobi counterterm in order to have a well-defined saddle point approximation. Further developments and extensions are commented upon in the discussion.