The real issue may actually be that scientific journals are result biased. A recent study on the effects of learning a second language concluded that it improve the ability to concentrate. The problem was that the same researchers did several runs of the study and only one got the result they wanted. The rest showed no benefit. But journals do not require disclosure of no result studies because they want to publish results. I wonder how many times these researchers pulled data and found nothing.
Also, I have never seen a study with a scientifically significant set of "vigorous" runners. The "vigorous" runners are usually classified as running more than 20 mpw at a pace faster than 9 mi per min. I know people who are 20-30 lbs overweight who can run 40 mpw at 8 min pace.
The other issue is that the alleged higher mortality may simply be that there are people with unknown congenital heart issues who are out there hammering it on the roads who should not be. If that is the case, the mortality issue may be a red herring for those with no pre-existing cardiovascular issues.
What is completely lacking in these studies is data on chronic disease and day to day health outcomes. It may be the case that runners check out earlier, but have fewer chronic illnesses and generally live much better, but shorter lives.