A treaty is a possibility. However, the circumstance between the Philippines is different from Cuba right after the Spanish American war. The Philippines can agree to naval/coaling station, give USA commercial advantages or sign a mutual defense treaty. But most likely the philippines would want to keep its right deal foreign relations with other countries.
In Cuba, U.S. Army literally did the work load. USA had complete control regardless if the Cubans wanted the treaty or not. The Cubans were also smaller both in population and natural resources.
In the Philippines, the situation of Cuba doesn't hold true. The Philippines essentially can reject the treaty without the American being able to do anything except fight a war.
A treaty to guarantee mutual defense, a navy base, and commercial advantages sounds like the best bet for this to work. The question now is, what is going to happen next, how will this change history?