Have you tried calling 'dbisql' with the '-nogui' option (along with -'c ...) and passing the script?
If you are using this to extract hundreds of thousands of rows then there is definitely something wrong here as other things, such as network traffic to the dbisql client, will impact performance (you can set a larger server packet size for this).
How often is this being performed? Are the 'reports' only extractions or the results of SQL queries? What is the destination system - is it another database?
Have they looked at other tools such as Data Services or SRS?
Chris