This science on this issue is very weak and a lot of the bashing on distance running comes from a single researcher who has suspect methods. The issue has also been used by crossfit, boot camps and other fitness fads to woo people away from marathon training groups.
There are a number of very credible long term studies on distance runners that generally show very positive overall outcomes. The main problem has been trying to study the serious, competitive runner. There are too few out there to get a good sample size. And then it is difficult to control for things like runners with pre-existing/congenital heart issues and runners who have crappy diets because they think the oven is hot enough to burn anything.
Physiologically, there is evidence of plaque build up on the hearts of marathon runners and triathletes who do Ironman length events. But this is not the same kind of plaque you get from eating donuts and playing video games all day.