Simple AutoHotkey script:
Run, %APPDATA%\Twitch\Bin\Twitch.exe ;path to Twitch binary
FindAndClose:
if WinExist("ahk_class Chrome_WidgetWin_1") {
WinClose
Exit
}
Goto, FindAndClose
Save to text file, compile to exe with Ahk2Exe compiler and put to autorun folder (type %APPDATA%\Microsoft\Windows\Start Menu\Programs\Startup into Explorer address bar). Don’t forget to disable autostart in Twitch settings. Also you need to enable “When I Close the App: Hide Twich” option.