Whether false positives or false negatives are more harmful is a difficult question. A false positive might stop millions from taking a life-saving drug. A false negative might cause millions to take a life-threatening drug.
By nature a false positive interaction could be re-tested more easily than a false negative though, correct? Also, that fits in with medical "first, do no harm" framework more readily.
Regarding your second point, I agree. But it must be balanced against the other tenets of medical ethics. At any rate, this seems to be an important study. I look forward to seeing the same study carried out across different EMR databases and then meta-analyzed. That will be extremely powerful.