The issue is that the CMS would have to understand how the database was laid out. Even having a different number of columns would prevent the CMS from understanding the structure of the tables. A CMS isn't a human. It just interacts with data how it's told, it doesn't ever interpret or understand the data.
Your best bet would be to first install a simple CMS with a table prefix (something like installing WordPress with "wp_" as the table prefix) to prevent it from over-writing any existing tables. After this you would need to write a plugin for the CMS which tells it how to read your database. It may be possible to find a plugin which already does what you want and then modify it to use your table design rather than the intended one.
In either case, though, the information in a database is part of the site's content. As such it's the job of the content management system to both create and maintain it. Creating it outside of the CMS will generally confuse it and require some work to integrate it.