In this paper study, we develop a Bayesian Network model selection principle that address addresses the incommensurability of network features obtained from incongruous datasets and overcomes performance irregularities of the Minimum Description Length model selection principle. This is achieved (i) by approaching model evaluation as a classification problem, (ii) by estimating the effect that sampling error has on the satisfiability of conditional independence criterion, as reflected by Mutual Information, and (iii) by utilizing this error estimate to penalize uncertainty in the Minimum Uncertainty (MU) model selection principle. We validate our findings numerically and demonstrate the performance advantages of the MU criterion. Finally, we illustrate the advantages of the new model evaluation framework on a tRNA structural biology example.