I'm no expert, but here's a theory:
Maybe marathoners can't safely take as much EPO as track athletes. EPO increases red blood cell count, making the blood thicker. This increases the risk of clots developing, which can be fatal.
In the marathon, athletes become much more dehydrated than in the shorter distances. This decreases the water content of the blood, making it thicker. Since marathoners on EPO already have thicker blood to begin with, the increased thickness due to dehydration may be excessively dangerous unless dosages are kept reasonably low.
Take for example Bekele's first fiance, who died during a training run, or some Kenyan marathoner (I don't remember the name) who died during a marathon. Both were likely on EPO, and both were likely dehydrated.
While lower dosages may be safer, they do not enhance performance as much as higher dosages. As a result, marathoners have not seen the same improvements from EPO that runners at shorter distances have.
If someone is an expert, please tell me if I'm wrong on this.