Yes, the Mishnah says that metzitzah is a necessary part of milah. Not because it’s part of the milah itself, but for the safety of the child. It also says putting cumin powder on the wound is a necessary part. Why don’t we still do that?
The Chasam Sofer was presented with a case where some children had become sick with sores. The Chasam Sofer said that just as cumin is no longer used because better methods were found to protect the baby, so too metzitzah could change if a better method is found. He says that it is not a part of the actual mitzvah, it is only to protect the child, and we want to use the best possible means to protect the child.