It sounds like the process that you used to update MediaWiki was not a good choice. It is not a good idea to upgrade software installed from package management by overwriting it with software from upstream. One of the reasons is one that you've discovered, but there are others...
So whilst you could manually remove the mediawiki package (apt-get remove mediawiki) and then install from upstream, I don't think that would be the best course of action. Personally I would recommend that if the version of MediaWiki included in the TKL Appliance is too old, then you would be better using the LAMP appliance and install MediaWiki from upstream to that.
Then migrate your data across. I suspect that initially it would be better to manually migrate the data. Once you have done that then TKLBAM will be fine for backups, but I think it might cause issues.
Remove the version installed by package management
It sounds like the process that you used to update MediaWiki was not a good choice. It is not a good idea to upgrade software installed from package management by overwriting it with software from upstream. One of the reasons is one that you've discovered, but there are others...
So whilst you could manually remove the mediawiki package (apt-get remove mediawiki) and then install from upstream, I don't think that would be the best course of action. Personally I would recommend that if the version of MediaWiki included in the TKL Appliance is too old, then you would be better using the LAMP appliance and install MediaWiki from upstream to that.
Then migrate your data across. I suspect that initially it would be better to manually migrate the data. Once you have done that then TKLBAM will be fine for backups, but I think it might cause issues.
If you choose to persevere