The .pak file is preferable over individual assets because it results in fewer web requests, allowing the assets to be loaded faster. The savings are especially apparent for people with slower connections. If you can work with the client to figure out what the problem is with loading the .pak file, that would be preferred.
Undoing the .pak output on your side will require a bit more work than putting a line in the openfl settings, and is only something that's possible for subscribers.
Copy the file at [stencyl install]/sw.jar/res/templates/project.xml to [stencyl workspace]/templates/project.xml.
(sw.jar can be opened as a zip file, and the templates folder will need to be created in your workspace.)
Then, in the copied file, near the bottom, find the line <library name="default" type="pak" if="publishing" /> and delete it.
We may offer options for determining how assets are packed (or not packed) in the future, but for now you'll need to make do with this workaround.