Downed woody debris in rivers, creeks and even "higher order, high elevation streams," is constantly in flux. At least every few years in all non-controlled (i.e. non damned) river systems, a natural disturbance called high water, shakes things up, rearranges the wood and generally changes the riparian habitat. This is a good thing in terms of wildlife habitat. It affords new oppurtunities for different animals and closes off others so that certain areas can repopulate. For instance sometimes a log can create a nice deep pool in an otherwise shallow creek and the fish habitat is generally thought to be enhanced by this, but when that wood moves it does not destroy the entire fish habitat for that section of river. The fish easily adapt to life in a differnet pool, fertilize their eggs elsewhere on the same stretch and the insects and micro-invertabrates that they were feeding on have a chance to repopulate.
In my opinion we (creek boaters) need to consider a few simple things when cleaning wood from runs and our impact cxan easily be minimized (at least in terms of wood removal - disturbing wildlife, eroding banks, etc. are seperate issues).
1. Only remove wood that does not allow room for safe passage. If the wood is not blocking the entire runnable channel than leave it be.
2. Only remove the section of log that is blocking the channel if possible. Just cut a slot a couple of boat widths wide and that should do the trick. This is usually easier anyway.
3. Be discreet. Using a chainsaw in the wilderness is illegal (at least in big "W," nationally designated wilderness), and it truly does disturb the wildlife. Remember all of the animals of the forest use the river for hydration and the noise created by chainsaws tends to scare them away (but like roads and other human impacts - not for long - they need the water and they will come back). Chainsaws cause by far the biggest impact in relationship to wood removal. Use hand saws and rope advantages where possible. When using a chainsaw concentrate its use. Do all of the cutting that you can in one day and then give the area some time before you come back to cut more.
These are my opinions and although I work as an ecologist I am not writing this as a doctoral thesis. I do however have a strong understanding of riparian ecology and the effects that human impacts have in riparian areas. I also own a creek boat and have removed a few logs from my favorite creeks.