Windows: How to cleanly stop tor process from the command line?

From comments:

If I may ask a question further from the above. Is taskkill bad for my system? Is it bad If I use it pretty frequently?

As long as you don't use /f it's no problem. Then what you're basically doing is asking the program "could you please shut down?". The program receives this signal and decides to act or not. A very typical thing that may happen is that you get a dialogue box with "Do you really want to quit?" or something like that. It's essentially the same as clicking the closing 'X' or pressing Alt-F4.

If you add /f it may be harmful in some cases, because that will forcibly kill the application. But on the other hand, if you cannot resolve the situation by invoking taskkill without the /f parameter, then the damage is often already done.

Usually, it's no big deal, but if you're unlucky, it could lead to things like corrupted files and such. But as long as you're only using user level applications, the risk of damaging your system as a whole is minimal. And I have a hard time believing that you could cause any major issues that cannot be resolved by just reinstalling Tor. I'd guess that the worst reasonably likely problems is things like corrupted downloaded files or something, but nothing major to the system.

TL;DR

taskkill /f /im tor.exe it NOT a clean way, but taskkill /im tor.exe is. But if the latter does not work, it's an indication that something is wrong, and it's possible that there simply is no clean way to do it.