Maybe I've watched Scarface one too many times, but I think the reason leaders of traditional drug distribution networks get life sentences is because they frequently resort to brutally violent means of running and defending their drug operations. Because they hold the supply of drugs rather than simply being a two-sided marketplace like the Silk Road, they have to physically defend that supply and the locations which house it (from rival organizations, the Police, etc). In a way, not only were the drugs being sold on the Silk Road safer, but the process of selling drugs was probably safer.
EDIT: This argument would probably hold up a lot better if Ulbricht hadn't tried to have people killed. sigh