Two options come to mind:

1. If your organization has any development capacity, it is not difficult to write a specialised importer using Applescript. This would give you the most efficient workflow.

2. For a quick and dirty solution in the interim, you can use search and replace to convert your CSV text into tab-delimited text, and use Omnioutliner to import that. Omnifocus can import Omnioutliner files.