A few points: The Gemara says metzitzah must be done. It does not say it must be done with the mouth. It just says there must be suction. We learn that it’s done by mouth because the Rema says that you spit out the blood into the dirt. (Not that the Rema is not cause enough to do it!)
As for the reasoning behind it, the OU writes the following on their website:
The Chatam Sofer went on to demonstrate that applying cumin powder is also listed in the Mishnah as something done even on Shabbat, yet no one argues that only cumin must be used as a salve for the area. Since the Talmudic era we have found more effective methods of achieving homeostasis and protecting the wound from infection, and this is why halachic authorities do not require the use of cumin alone. Similarly, contended the Chatam Sofer, based on the Mishnah, no one could argue that the mouth alone had to be used to suction the blood.
12. This letter was first printed in 1845 by Menachem Mendel Stern in the periodical Kochvei Yitzchak. It is quoted in a number of secondary sources, including Rabbi Rami Cohen, Bris Avraham HaKohen (New York, 1993), 192.”