Application.Quit() should normally terminate Inventor. If it does not happen, try kill the process using .NET System.Diagnostics.Process.GetCurrentProcess().Kill()
From MSDN: Note that the Kill method executes asynchronously. After calling the Kill method, call the WaitForExit method to wait for the process to exit, or check the HasExited property to determine if the process has exited.
Visit MSDN Process.Kill site for more information.
