You mention most of the pros and cons of utilizing the large tree branches. There has been published research that the branches do improve the quality of the fishery for both forage and predator. One other pro is the branches are surface area for growing communities of attached algae and associated invertebrates that increase and enhance the productivity of the pond. It is for you to decide weather the branches are to go or stay. Or compromize and decide how many should stay. My only suggestion is to allow some with the large end on shore so they can be more easily removed (draged out) when needed.