Where do they believe otherwise? They're merely mentioning that the city was populated prior to the genocide. You're defending atrocities against a specter of your own imagination.

Why do you feel the need to defend against the horrors of colonialism?

We then had to fight the Philippine Republic for control of the country, in the Philippine-American war.

What's wrong with an emotional response to an atrocity? Is it irrational to cry over the Holocaust because, hey, the Tsars didn't some pretty bad pogroms, too? No, emotional responses are perfectly fine and are a normal mode of thinking. Your fetishization of reason is dangerous and echoes the same rhetoric that enabled these atrocities: oh, they're not people, they're savages because X, so cut off their hands if they don't bring enough silver. The correct response here is to denounce colonialism, not to say, "oh, hey, it's not that bad because other people have done bad things."

The point is that it wasn't just Europeans that have done bad things in the past. It was every type of person. And now we can collectively move past with the lessons.