We use a nonlinear master equation formalism to account for thermal and disorder effects on spin-dependent electron transport in helical organic molecules coupled to two ideal leads. The inclusion of these two effects has important consequences in understanding the observed length and temperature dependence of spin polarization in experiments, which cannot be accounted for in a purely coherent tunneling model. Our approach considers a tight-binding helical Hamiltonian with disordered onsite energies to describe the resulting electronic states when low-frequency interacting modes break the electron coherence. The high-frequency fluctuating counterpart of these interactions, typical of intramolecular modes, is included by means of temperature-dependent thermally activated transfer probabilities in the master equation, which lead to hopping between localized states. We focus on the spin-dependent conductance and the spin-polarization in the linear regime (low voltage), which are analyzed as a function of the molecular length and the temperature of the system. Our results at room temperature agree well with experiments because our model predicts that the degree of spin-polarization increases for longer molecules. Also, this effect is temperature-dependent because thermal excitation competes with disorder-induced Anderson localization. We conclude that a transport mechanism based on thermally activated hopping in a disordered system can account for the unexpected behavior of the spin polarization.