You seem to have covered most of the conceivable options. Outside of the ones you mention (other than letting Japan have the Philippines) the only other choice would be for the US to exercise some degree of control over the Philippines.
The options that faced McKinley, then, would have to do with how much control to have of the Philippines. The US could have let them be essentially independent but could have controlled foreign policy and defense. On the other side of the spectrum, the US could have made the Philippines an actual part of the US, making one or more states out of the islands. Or he could have taken some other position along that spectrum, giving more or less control of the Philippines to its people.