I would caution against taking quotes out of their historical context. There has been a recent surge of politically motivated popular history meant to paint Theodore Roosevelt as the world's greatest human rights abuser responsible (directly or indirectly) for the greatest atrocities of the 20th century, and by extension argue that the US strategy during the Philippine Insurrection was essentially predicated on a policy of war crimes. That nonsense aside, the leading academic historians of the Philippine Insurrection - John Gates, Brian Linn, David Silbey - all agree that the accusations of counterinsurgency predicated on atrocity and war crimes is vastly over-exaggerated. Linn, for example, looks into and refutes the claim that the water cure was used anywhere near the number of times reported. Cases like that of "Hell Roaring Jake" Smith and Major Waller and the Balangiga massacre on Samar are the exception, as noted by the fact that they were court martialled for their actions. Smith was forcibly retired, while Waller was acquitted in no small part because it was agreed an Army court had no jurisdiction over a Marine.

Very generally, the Philippine Insurrection was actually characterized more by the difference between those generals like Elwell Otis on the one hand, who believed the country was mostly pacified because there was no violence, and started pouring reconstruction money into the pockets of the insurgents that controlled the town, and on the other Arthur MacArthur, who recognized more of a need to control the population and isolate the insurgents. He did this by means that are less than acceptable to use today, like population movements and burning crops, but they hardly amount to an official policy of atrocity or war crime. More importantly, they were meant to achieve effects (isolating and identifying the insurgents) that are still important today, and which can be done in more palatable ways to get a similar outcome.

I would recommend reading:

Schoolbooks and Krags (John Gates)
The US Army and Counterinsurgency in the Philippine War (Brian Linn)
The Philippine War (Linn)
A War of Frontier and Empire (David Silbey)