We theoretically analyze the effect of probe beam intensity on all-optical switching based on nonlinear absorption, using the pump-probe configuration. To draw general inferences that are applicable to a wide range of polyatomic molecules, we consider as a typical example, switching in pharaonis phoborhodopsin (ppR) protein and its mutants that exhibit a complex photocycle similar to bacteriorhodopsin (bR), having a number of intermediates with respective absorption spectra spanning the entire visible region. The switching of the transmission of a cw probe beam by a pulsed pump beam has been studied in detail at different wavelength combinations. Interesting consequences emerge from the present analysis. It is shown that by controlling the probe intensity, the switching characteristics can be inverted, switching time can be reduced and the profile of the switched probe beam and the switching contrast can be controlled. For some cases, the switching contrast can also be maximized by optimizing the probe intensity. Increase in probe intensity also leads to increase in switching contrast under certain conditions. At particular spectral and kinetic conditions, the nonlinear optical material appears linear for a given probe intensity and pump-probe wavelengths, respectively. Variation in probe intensity thus provides an effective means to modify the switching characteristics instead of using mutants with different rate constants for a variety of nonlinear absorption based all-optical devices.