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Yes, since it was installed outside the package tools you can only delete it the same way...
I would look at the original tar archive and make sure it created everything under a single parent directory, then delete that directory. If it created more than one parent make sure you get them all - AND make sure it did not create any files in pre-existing directories.
If the runtime of the program created any configs in /etc/ or ~/, you will need to find and delete those separately.
If there looks to be a single directory then you are probably safe to just remove it and all its children.
I always like to take baby steps when doing such things to keep from doing anything unexpected, so I would...
Code:
cd /opt - Change into the parent directory so you can delete with relative paths...
pwd - Just to confirm that you are where you think you are...
ls wkhtmltox - So you can see what to expect... then...
rm -rf wkhtmltox
ls - To confirm that it is gone...
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