Firstly, moral sin, that sin which separates us from eternal life with God requires not only that the action be gravely wrong, but that the person knows it to be wrong, and freely chooses to do it. One could agree that his treatment of the native peoples was at times wrong, and simultaneously say that it was probably not a sin because he did not understand it to be wrong. We should always be careful not to retroject 21st century standard onto persons of prior ages. In every generation we can only work with the information that we had.
More importantly, we miss the point if we think that by declaring a person a saint, we are saying that they were without sin. Apart from Jesus and Mary (because of th unique gift given her) we are all sinners. Of course, Junipero Serra was a sinner and so are all of us, but we also hope to be saints like him one day.
While we acknowledge his imperfection, today we celebrate not only the good that he did, but the good he has inspired and continues to inspire in others. We believe that by God's grace he stands with all the holy men and women around the throne of God, and we pray that we will have that same passion for spreading the Good News.