Well first option would be to find another ISP if they won't modify the settings to work correctly with your software.
A more technical fix might be to make some changes to moodle code. I noticed there are some commands in the cron.php or perhaps a file referenced from it that adjust the max memory usage and time to run. Perhaps this technique could be used to modify the upload limits as well. It would however I think require editing several files to make the changes. Perhaps give your ISP an ultimatum. Change the setting or you will find someone else to do business with.