I have an idea. Lets prioritize transactions by amount of nano sent. Bigger amount - higher priority. If someone is trying to send a big amount back and forth there will be a delay anyway as the second transaction needs to wait for the confirmation of the first one. Or there could be some artificial delay by the protocol to send nano further you have wait a certain interval after it's cemented into the ledger and fully synchronized with <50% nodes. So it means if someone is willing to hurt the network with spam must own a huge amount of nano, which is very unlikely to damage your own network you invested.
Those micro amounts spammed will be left unconfirmed forever. And we should not care about those transactions. They even can be deprecated and rejected by nodes after the certain time.