Opamp input impedance on high frequency
As you suspect, the input capacitance will be forming an RC low pass filter with the resistance.  

Let's assume 2pF for the input capacitance (reasonably typical for a FET input opamp)  

With your 681k resistor it will form a filter with a -3dB point of:

1 / (2pi * 681k * 2pF) = ~117kHz  

So the square wave of 125kHz will not look very square at all, since it's harmonics will be attenuated.  

Note this does not include any additional capacitance from your layout (traces etc)
As Olin points out the actual rolloff frequency is likely to be quite a bit lower (how much depends on your layout)

The input impedance of a non inverting FET opamp will be very large anyway (> 100 Megaohm)
Why do you need the 681k resistor?  (a schematic of your setup would help)

If you do need the resistor (e.g. as part of a voltage divider) then you can add a small amount of capacitance across it to compensate for the roll off (you will need to do the calculations to work out how much)
For examples of this, I suggest googling for/looking at oscilloscope input circuits.