Although numerical studies modeling the quantum hall effect at filling fraction $5/2$ predict either the Pfaffian (Pf) or its particle hole conjugate, the anti-Pfaffian (aPf) state, recent experiments appear to favor a quantized thermal hall conductivity with quantum number $K=5/2$ , rather than the value $K=7/2$ or $K=3/2$ expected for the Pf or aPF state, respectively. While a particle hole symmetric topological order (the PH-Pfaffian) would be consistent with the experiments, this state is believed to be energetically unfavorable in a homogenous system. Here we study the effects of disorder that are assumed to locally nucleate domains of Pf and aPf. When the disorder is relatively weak and the size of domains is relatively large, we find that when the electrical Hall conductance is on the quantized plateau with $\sigma_{xy} = (5/2)(e^2/h)$, the value of $K$ can be only 7/2 or 3/2, with a possible first-order-like transition between them as the magnetic field is varied. However, for sufficiently strong disorder an intermediate state might appear, which we analyze within a network model of the domain walls. Predominantly, we find a thermal metal phase, where $K$ varies continuously and the longitudinal thermal conductivity is non-zero, while the electrical Hall conductivity remains quantized at $(5/2)e^2/h$. However, in a restricted parameter range we find a thermal insulator with $K=5/2$, a disorder stabilized phase which is adiabatically connected to the PH-Pfaffian. We discuss a possible scenario to rationalize these special values of parameters.