I would suggest turning all chinese fishermen into armed Militia, give them automatic rifles and RPG. They would only use when encounter hostile forces trying to kidnap them such as the filipino armed men.
China has a lot of fishermen and 10,000 fishing boats. And if each of them are armed, it would be force to reckon with.
After the fishing trip they would return the weapons to authority.
So, they get weapons when the trip started and return them when coming back.
US military act as a stabilizer to the Philippine nation, without it, easily become a fail state with that many islands and insurgencies, rebels running around. Really, Philippine could fall apart anytime soon and become another Somalia and you have pirates situation there. The country is just 1 step away from chaos and you'll have looting incidents and burning of factories, riots. So economic considerations have to be taken. Long time ago, that island nations area are infested and haven for pirates. US and Philippine each year have to do special operation to cleanse those muslim rebels and pirates. The protection of shipping is actually crucial and true fear\concern of US not from the Chinese fishermen but actually from the Philippines pirates and we don't need armed fishermen from China to cause more troubles. Civilians should not get involve and let each nation coast guard deal with it.