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How did you install TOR in the first place? It looks like you did not use apt-get, but apt-get is not perfect on removing something. You can always manually remove it (or any program). Specifically with TOR, go to /usr/local. There is a symlink there (tor) and a directory tor-browser_xxxxxx. Delete the symlink and mv the directory to some other name the system won't recognize. See what happens when you try to start tor.
There may be other files elsewhere so you may get some errors, but it shouldn't start. There is probably an item in the menus to delete. There may be some configuration files somewhere in you home directory. A general search with find can help with that. Be careful of deleting more than the directory and symlink though. Make sure you are not affecting anything else.
If all goes well, you can delete the directory name you moved the original tor directory to.
Installing through a package is not non-standard. It has been while since I installed tor, but it seems to me it is done through a deb package of theirs, or else it is a tar.gz file, which usually makes it fairly simple to uninstall manually either way. Apt-get, aptitude, etc are simply simplifications and extensions of the dpkg process. The packages are usually maintained by volunteers, not the software writer him/herself. As a result the repository packages can be and often are one or two releases behind. In most cases this is not important. In some, especially security related issues, it can be VERY important. Tor falls into the latter category in my opinion, so I do not rely on repositories but on tor itself. And, I believe, though I am not sure, that all that has to be done to uninstall is delete the /usr/local package.
I agree with you on standard/non-standard, but I think my definition of standard may be broader than yours.
I do not like programs that use non-standard methods of installation. I consider that sloppy programming.
in the case of the tor browser package, this is by design and not sloppiness.
it sets up its own environment (jail) in ~/.tor_broser_* and runs inside that.
even if you install it through your packet management, that is what the package will do.
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