You should have no problem to run this type of task via cron jobs, as @Ranty says there is no timeout, in CLI the maximum execution time is set to unlimited.
The time that it will take depends on your server, the time to retrieve the csv that you will attach... as @Ranty says is a good choice to run your cronjobs at night.
And finally yes, if you are using CI why not use the codeigniter's built in email class? For running scripts via command line read this: http://ellislab.com/codeigniter/user-guide/general/cli.html