You can create scripts to move the files to the correct location if the compressed file has a different structure. Check the enemy territory etpub mod for an example.The file is extracted to __tmp. There is a script for the "after extracted" event that moves the files to the correct folder.
Using a similar script you can create a dummy zip file with no files. In the after extracted event download the file, extract, then move the files to have the correct structure. Just 2 extra lines to download and extract the file.
Having you allow to enter a url in the mod settings sounds good but then you have the risk of somebody changing that url so it downloads malicious files. There would have to be a way to disable that since some hosts need to protect ventrilo and ranked files.