Stop Safari from appending ".download" to not fully downloaded files
I don't know of a way to do it, and if I did, I would not recommend this at all. First, because trying to work with partially-downloaded files is a good way to get yourself into trouble. Depending on how the programs you want to use on the file work, they may or may not cope with having the file modified as they're trying to use it. A media player, for example, might check the file's integrity before playing it, and refuse to play a damaged file. Or it might note the file's length (when it opens it) and assume that's the length it'll always have. Or it might read the entire file into memory (as it exists when opened) and then play that without going back to see if it's gotten longer. Or... lots of things might go wrong.

The other problem is that that .download file is not actually the partially-downloaded file. It's a Finder package: a folder with hidden contents that the Finder treats as a regular file. You can see its contents by Control-clicking (or right-clicking) on the .download file, and choosing Show Package Contents from the shortcut menu. Inside it, you'll see an Info.plist file with information about the download (you can select it and press Command-Y to see the info in XML format). You'll also see the partially-downloaded file, under its regular name.

If you really want to do something with the partially-downloaded file, that file inside the .download package is what you want, and it's already going to have the correct name. But again, I don't recommend this for the reasons in the first paragraph.