The copper sulfate will eliminate the FA but the long term side effects won't be beneficial. The vast majority of the CS you use to treat the FA will end up on the bottom of your pond and take every beneficial plant and organism with it. Eventually, if you use it often enough, it will be the only alternative you have until you dredge the bottom.
Whether you use it or not, you should remove the FA manually. Using CS and letting all that plant matter decay at the bottom is a good way to crash your dissolved oxygen.
