It's not that the mohel is actually intending any harm to the child or that they are actually a pedophile that's the problem. The problem is twofold.
One, that it directly resembles an act of pedophilia. Even though the mohel is not getting any kind of sexual enjoyment from it, the resemblance is a problem enough in itself. Sometimes appearance really does matter regardless of intent. These rabbis are not pedophiles, and do not intend any harm to the babies. However the fact that such an act done by anybody else in a different context would be considered to be criminal pedophilia should give people pause at the very least. You want to avoid the appearance of unrighteousness even if nothing harmful is actually going on.
The second, and arguably more important reason, is that this act can cause permanent harm through infection. Herpes is not curable. It's a life-long, painful, and contagious disease. Other viruses and bacteria can also be present in the human mouth, and contrary to what some people might think, mouthwash just reduces the number of bacteria in the mouth, it by no means makes the mouth sterile.