In a facility setting, I would say that the coder can code exactly as the documentation reads, based on AHA and WHO guidelines and other regulatory guidance. However, if you work for a physician practice, or anywhere that physicians are compensated based on RVUs, then you would definitely want to have a policy about this.
Our physicians receive a bonus (in addition to salary) based on the number of work RVUs obtained over and above the expected threshold. This means that higher level E&Ms and/or more visits will garner them a big check at the end of the year. In instances like this, having a coder change the code that they have selected or submitted may hit their pocketbook. Now I'm the first to tell you that this is not the best way to reward physicians, but it is what it is....in many organizations. However, our organization is also extremely committed to compliance, so our policy is that the coder/auditors may change codes based on the documentation that accompanies the charge, regardless of what the provider wished to bill. If that's what you decide do, be sure to get it in writing.
Coders in small practices, or those working for physician groups without such a policy would be best to not change codes, particularly because the physician's name is on the claim form....not the coders, and there may be financial implications for the provider if you down or up-code them without their permission. But it's definitely something you should bring up for discussion--along with the risk of potential fraud, insurance take-backs, and other headaches that they might not be considering when all they worry about is their bonus check. If providers are educated properly about coding, and learn to trust their coder, in my experience, providers will leave it all up to the coder, because they just don't want to deal with it.