OK well first of all, any time you move anything around in your pond it's going to kick up some pond dust (we'll call it muck for lack of a better word). This is normal and will generally either settle back down in a couple hours, or be picked up by your mechanical filters. Secondly, if you had more of a timely scheduled for scooping up the leaves and needles in your pond, as I mentioned earlier, you would likely be able scoop a lot more of it up before it actually breaks down into that fine muck that is a lot harder to scoop out. Of course, as I also mentioned earlier, a pond designed with a good functioning skimmer and bottom drain would eliminate much of the need for manual pond cleaning.
It really comes down to the design of your pond, but removing all your fish and completely draining your pond every year is stressful on your fish and can upset the bio-balance of your pond, meaning you pretty much have to start from scratch every year.
It takes years to develop a really healthy coat of algae and nitrifying bacteria on the surface in your pond, and wiping them out every spring seems like a huge shame.