Marijuana can help runners disassociate from pain and can trigger similar feelings to the runner "high".
I was a fairly decent D1 XC/T&F runner: (1:52, 3:53, 25:03). Never smoked in college, started after I "retired" from running. I was burnt-out and found that without running, I was full of energy and anxiety. In some ways, smoking replaced running. I became very successful in my career and maintained my physical fitness, to some extent, with other forms of exercise.
After nearly a decade on the bench, I've taken to running competitively. Smoking helps with my mental recovery, which in turn helps my physical recovery. Ever have anxiety before a race? Ever have digestion issues? Trouble sleeping? Discomfort from overtraining? Lack of appetite? Physical exhaustion?
Well, IMO marijuana helps those issues that runners commonly face. Sure... if you fail to filter the smoke, your lungs will have some work to do. Just the same for runners who workout near major roads or those that run in big cities like New York or LA. Could you imagine training near Mexico City? There are plenty of options for filtering pot smoke. Perhaps we should focus on local air quality issues, before we consider the harm that comes from few puffs of smoke.
As for negative feelings that some users feel. Those vary widely. Modern strains have been developed to address specific psychological reactions. I personally prefer organic indica strains. With the ideal strain, I have absolute mental clarity and simply receive a calming benefit with a slight uptick in my mood. Pre-run, post-run, during your run... it's all fine.
Alcohol is so much harder on my body. I drank every week in college, while running competitively, and no longer touch the stuff. In hindsight, I wish I didn't drink while running in season. I was really harming my internal organs and overall health. Alcohol is a poison.
MJ is a medication. Chill out, smoke a fatty, and hit the road.