You didn't misunderstand. A sudden stretching of space cannot change the number of peaks and troughs as they go past, but since those peaks and troughs are now slightly further apart, the frequency of the light is slightly lower, and the light takes slightly longer to travel. This applies to light that is already in transit. Of course, as the gravitational wave passes by, the length/frequency returns to normal again.
New light that is emitted at one end of the journey while there is a stretching status will have the same frequency as normal, and just see the longer journey. In fact, the gravitational waves that LIGO is able to detect are slower than the time it takes for light to make the journey, so the stretching is effectively gradual, and the detector is basically an extremely accurate length measurement. The gravity waves aren't fast enough to make the light changing frequency a thing that needs to be worried about.
New light that is emitted at one end of the journey while there is a stretching status will have the same frequency as normal, and just see the longer journey. In fact, the gravitational waves that LIGO is able to detect are slower than the time it takes for light to make the journey, so the stretching is effectively gradual, and the detector is basically an extremely accurate length measurement. The gravity waves aren't fast enough to make the light changing frequency a thing that needs to be worried about.