Sinusoidal Waveform Induced on Long (~15m) Wire
I'd bet that if you disconnect the wire at the MOSFET then you'll still have the 1.3 MHz at the pullup resistor.  If that is the case then your wire is acting like an antenna and you're receiving something.  

Sources of radio waves tend to change.  This could be why you haven't seen this before.  Or, you never used this kind of wiring harness before and so never tried an "antenna tuned to 1.3 MHz" before.

There is not much you can do with this to fix it.  At least, not much that doesn't have some negative side effect.  

One solution is to put an RC filter just before the pullup at the input.  Size it so the cutoff frequency is as low as possible without effecting the speed at which you can measure the cable.  It might be that you can't do it without effecting the speed, those are the breaks.  

Keep in mind that the R from the RC, and your pullup resistor will form a voltage divider.  When the MOSFET is on, and the wire is 'low', then the R+Pullup will limit how low the voltage on the input will go.  Make sure that the R in the RC is low enough, or raise the value of the pullup, so your input will go low enough.

Another possibility is that you are exciting some sort of resonance in the wire.  This is unlikely since the speed of the signal traveling down the wire and back is much faster than 1.3 MHz.  But if it were a problem then I would look at putting a resistor in series with the MOSFET.  Basically something to slow down the falling edge of the signal.