It all depends on his motivations and goals. If his intention was to help the Philippines achieve independence from Spain he was only supposed to provide military assistance and then help Filipinos establish a sovereign, independent state. If on the other hand, his goal was to score a victory for the ideology of the Manifest Destiny of American Expansionism and add the Philippines as another US territory like what had been done with Hawaii (which would give Americans an unbeatable foothold in the Asia-Pacific region), then taking over the Archipelago was consistent with that strategy. The situation was very complex. President McKinley was not a staunch expansionist. American opinion was divided, business circles supported annexation of the Philippines but other parts of the population were against such move for different reasons (anti-imperialism, concerns over a non-white population being turned into American citizens by virtue of military conquest, etc.). The results of his policies were mixed. Americans did retain control of the Philippines but lost many lives and money fighting a Filipino insurgency for decades. Also, the image of the US was seriously degraded as it was considered hypocritical for them to pretend that they had broken with the British Empire to be a free, sovereign republic and then had become an Empire themselves towards other peoples. Their navy was able to station in the Philippines and Americans were able to trade and profit as well and having forces in the area would prove extremely useful during WWII but McKinley could not possibly know that major country would occur in the area 30 years into the future.
