Studies on the propagation of malware in mobile networks have revealed that the spread of malware can be highly inhomogeneous. Platform diversity, contact list utilization by the malware, clustering in the network structure, etc. can also lead to differing spreading rates. In this paper, a general formal framework is proposed for leveraging such heterogeneity to derive optimal patching policies that attain the minimum aggregate cost due to the spread of malware and the surcharge of patching. Using Pontryagin's Maximum Principle for a stratified epidemic model, it is analytically proven that in the mean-field deterministic regime, optimal patch disseminations are simple single-threshold policies. Through numerical simulations, the behavior of optimal patching policies is investigated in sample topologies and their advantages are demonstrated.