Não parece que os repositórios de APT do Debian tenham a versão mais recente do MySQL. E como você quer que ele seja mantido pelo APT, ao invés de instalar a partir do código-fonte, você pode usar o reposistory oficial do MySQL. Existe um pacote deb para a instalação do APT aqui , com instruções curtas
Primeiro, adicione o repositório do MySQL APT à lista de repositórios de software do seu sistema. Siga estas etapas:
Go to the download page for the MySQL APT repository at http://dev.mysql.com/downloads/repo/apt/.
Select and download the release package for your platform.
Install the downloaded release package with the following command, replacing version-specific-package-name with the name of the downloaded package (preceded by its path, if you are not running the command inside the folder where the package is):
shell> sudo dpkg -i /PATH/version-specific-package-name.deb
For example, for version w.x.y-z of the package, the command is:
shell> sudo dpkg -i mysql-apt-config_w.x.y-z_all.deb
Note that the same package works on all supported Debian and Ubuntu platforms.
During the installation of the package, you will be asked to choose the versions of the MySQL server and other components (for example, the MySQL Workbench) that you want to install. If you are not sure which version to choose, do not change the default options selected for you. You can also choose none if you do not want a particular component to be installed. After making the choices for all components, choose Apply to finish the configuration and installation of the release package.
You can always change your choices for the versions later; see Selecting a Major Release Version for instructions.
Update package information from the MySQL APT repository with the following command (this step is mandatory):
Em seguida, instale normalmente usando sudo apt-get install mysql-workbench