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Setting "Fail backup on upload failure" to Yes in the Configuration will delete the local files of the failed upload right away. The downside is that in this case you are left with no backup.

Another alternative is to set the Enable Count Quota to Yes and set Count Quota to 1 under "Local Files Quotas". This will delete the local files of the failed upload after the next backup is taken.

Which one you should use depends on your available disk space, and how much risk you are willing to take.

I suspect your question is how you can enable the local files count quota and set its value to 1 across different backup profiles and dozens of sites. My recommendation would be using an automation tool such as Ansible or Puppet and our WP-CLI integration which allows you to set values on individual settings on each backup profile.

Run wp help akeeba on your site (assuming WP-CLI is installed in your $PATH as wp) to see all the available commands. You can experiment on a test site and create reproducible steps. Remember that the commands which read the profiles and configuration can return raw JSON using the --format parameter. If you've used Ansible you immediately understand why's that. For other workflows, including writing custom shell scripts, you can always use raw text output and standard tools like awk and grep.