The great tragedy in this is that flows of many tributaries streams appear to be healthy. There are probably some individual tributaries to the upper Big Hole River with flows higher than 10 cfs--if that flow is measured up on the Forest Service lands above tributary diversions.
Yes, there are many, many, many diversions that occur high up on the tribs, long before the water has any chance to get to the main river. Unless and until the Big Hole Watershed Committee and the state agencies start paying attention to what happens up on the tributaries, no amount of water conservation on the main stem of the river will help grayling.
For example, here is a photo of a tributary diversion ditch high up on Forest Land--in fact, it's in the Pintler Wilderness. As of late last week, this ditch appeared to be taking at least half the tributary creek's flow. Worse yet, there are more diversions below this point.