Now, I've only ever installed it from ninite.com, so I know it didn't initially have the Sourceforge trojan/adware junk. However, I've since allowed it to download its own updates instead of doing it manually through the Ninite downloader. I've never, ever seen a program I've uninstalled via the Windows Control Panel with the ability to force a shutdown or restart without first notifying me or giving me the option to postpone. I'm starting to think there's something nefarious in Filezilla itself, perhaps in one of those "direct from the developer" updates, not just the Sourceforge wrapper.
Another interesting thing is that the built in Filezilla updater will first uninstall the app before reinstalling the updated version, and it never tried to restart or shutdown the computer during those updates, only during uninstallation from the Control Panel.
 Ninite strips out any malware or other crap from the installer and only installs the pure program with default settings, in the background, and sources the app directly from the developer's site when possible. It's my go-to tool for essential Windows utilities.