Maybe the solution is to make it a choice for the user? An option to "clean up documents when space is low on the device" in the instapaper options. If checked, stuff gets stored in cache. If not, in documents.
That way, the default behavior is that "download something = want to keep it on device", but users can do the other one too if they want. I don't think the option is particularly useful, but it might make the app reviewer happy?