Just random stuff, but yes, kill the willows. I use Tordon on the cut trunks, but there are cheaper methods.
At this point, I would personally only treat the broadleaf weeds above the shoreline with a 2 4-D like Weedar 64, and leave the rest alone. It's rated for land and water, so runoff should not be an issue. Broadleaf plants usually create shade, and shade would keep any seeds you may plant from growing. Something to consider is that algae will probably grow when the terrestrial plants below the shoreline are submerged, and start to decay. On a 5 acre pond, I wouldn't think it was a major issue, but it is a consideration.
