If you want a proper relational database, sqlite would suit better. There are GUI tools to work with sqlite database files and sqlite has csv import and export. But that won't help much if you already have a large CSV you just need to edit a few rows on.

As for versioning sqlite data, just don't ever update or delete any rows but instead only ever insert the updates as a new row. Potentially you could add a 'deleted' boolean and 'inserted' date columns to the tables you want to version. That way you can use '... and deleted = false' to filter out old data and you also know when updates occurred.