Only idea I have so far is to use an OpAmp and wire it as a comparator yourself (with some Rs). Here you are free to choose your required hysteresis.
As it turns out, it was easier to just add some capacitance across my two signals to filter out the noise. I now get a nice clean output from my LP Comparator.
Was an interesting exersize to go through. Sometimes you just gotta fight these things with hardware ;-)