I am far from an expert on game theory, but it seems that the cause of the tragedy of the commons is that people can use the shared resource for free. If there was a price to be paid, and the price was dynamically adjusted depending on conditions, then the overuse could be avoided.

Similarly for file storage and "reserving" it by creating huge but useless files. If everyone was charged a fee per gigabyte per day, then people would be less likely to create those placeholder files. You probably have to be careful about how you measure, otherwise you'll get automated processes that delete the placeholder files at 11:59pm and create them at 12:01am.