So, a deep, narrow trough, that's too narrow to pedal in without hitting the sides? I think going to a smaller pedal might find you hitting your shoes on the sides
It might just be too tight to ride through.
Depending on how long and steep it is, you could 'ratchet' to get through it: basically starting from 'ready position' you rock your leading pedal between 1- and 4-o'clock to kind of scoot the bike forward without making a full pedal stroke. I use it in rock gardens, root ladders, or water crossings, anywhere you don't want to get your pedals too low. The drawback is that you have to build enough momentum on each 'kick' to carry through the 'ratchet back' for the next one.