I think this is already solved to handle the small cost of Put request. If I remember correctly the idea is to have a special account linked to your normal account to handle the fraction of 1 Safecoin. The cost of PUT is taken from that. When it’s depleted you need to recharge it. When you recharge it a Safecoin is taken from your wallet and the amount inside the special account is set to 1.
The same can be done to handle microtransactions. You could send a micro amount of Safecoin from your special wallet to another user’s special wallet. When it fills up to more than one Safecoin, a new coin would be created and sent to the user’s normal wallet.
This way, you don’t need a file for every micro amount of Safecoin. Just a special wallet that keeps track of your spare change.