To remove the Apparmor profile from your system, you should use "apt-get purge" in place of "apt-get remove".
But it looks like you are using an older version of Tor Browser (3.xx), The directory structure has been changed in version 4.xx.
That seems strange, because there should be a warning from whonixcheck, the last lines in the result window should show:
WARNING: Tor Browser Update Check Result: Installed Tor Browser version...
To check Whonix version, find in the same window:
INFO: Whonix News Result:
√ Up to date: whonix-workstation-packages-dependencies 1.x
√ Up to date: Whonix Build Version 9.x
where Whonix Build Version is you installed version.
To check and update Tor Browser, please run:
Start menu -> Applications -> System -> Update Tor Browser