I can accept the botched chain of custody calls the test into question. If we are going to rely on a scientific test to be the sole arbiter of a man's livelihood, then the evidence has to be handled properly, and the prosecution has to be clean, too. If this were a $5MM fine, or whatever 1/3 of Braun's salary is, and it were assessed against a company with $15MM revenue, you can be darn sure that any competent K Street firm would raise the defense in an EPA, OSHA, or DOD contract case.
As for Braun, this will not clear him in the verdict of public opinion. Not only that, depending on whether he can be disciplined for the same subject later, he might not even be able to come out and say, "this was inadvertent, I did not intend to do anything except treat my herpes." If there is no limitation on bringing this back up (it is private, not criminal, so it depends on the MLB player agreement), the second he tries to make an excuse, it is an admission that the test was correct. Even if he can come out with the herpes medicine excuse, he's still tarnished in the eyes of most people.