_Import the CSVs into an sqlite database and run a DELETE query on it. Then use the database for further queries and throw away "The Art of Unix Programming"._
It's funny.. I'm working on a project with someone else who is creating a similar app and he went with the SQL approach. Because of the abstraction of the database he misses tons of problems in the data. Meanwhile with my clear text files and unix tools I'm constantly finding new ways to explore the data and find problems. It just depends what you're doing and what's important. The speed issue isn't a big deal.
