In my book, a doctor doesn't get to absolve themselves of responsibility by saying "just following orders" and that it's the investigative system that needs to be fixed. If they know the system is broken, it's both immoral and a deep betrayal of trust for them to report people without strong evidence.
Almost any injury can be framed as possible evidence of abuse. Parents shouldn't have to be afraid that taking their kids to the hospital after an injury will get them taken away. The vast majority of injuries are not from abuse, so a system with a low bar for evidence is going to end up with more false positives than cases of abuse. This is exacerbated by the fact that abusers, for obvious reasons, are often going to avoid getting medical care for the kids they abuse.
If your reasoning were applied more broadly, we'd put anyone accused of a crime, or of even planning a crime, in prison immediately, since otherwise crimes will occur (with people hurt/killed) that could have been prevented. There's a reason the legal system doesn't work this way.