Apply the important parts of the exit fix (#20607)

Windows/EmuThread.cpp

@@ -312,7 +312,6 @@ void MainThreadFunc() {
 		Core_StateProcessed();
 		NativeFrame(graphicsContext);
 	}
-	Core_WaitInactive();
 
 	g_inLoop = false;
 

Windows/MainWindow.cpp

@@ -1142,8 +1142,8 @@ namespace MainWindow
 
 		case WM_DESTROY:
 			InputDevice::StopPolling();
-			MainThread_Stop();
 			WindowsRawInput::Shutdown();
+			MainThread_Stop();
 			KillTimer(hWnd, TIMER_CURSORUPDATE);
 			KillTimer(hWnd, TIMER_CURSORMOVEUPDATE);
 			// Main window is gone, this tells the message loop to exit.