They do have a relation to capital - they are often at its creative source. (ex. scientists actively work daily to create new ways of taking plant medicine and manipulating it so that Bayer can get rich selling a new type of aspirin, or the scientists who work for Monsanto, or who invented those ugly toe shoes...)
But, what I dislike them for more, is their relation to 'fact', they serve the role that the priest class used to. They inform the public as to what is truth, and what is not. Their existence and social power reinforce that we can not rely on our own experiences and senses to determine reality, that all truth must be interpreted and 'proven' by an appropriate authority. They tell us that only they, the scientists with their special tools, can interpret reality, not unlike the priests who had the special ability to interpret god's will and translate it for the masses. And, much like the priest, their position within society, as well as their paycheck, rely upon those with the resources at their disposal to support them. So, those who inform us of how the world works, of what our bodies are capable of, of how we need to manipulate our body and world to 'be healthy', of what the future hold, comes from scientists who have loyalties. It is not just scientists who aren't impartial. Science itself, as dogmatic empiricism, can't except any view point that it can't control or understand or recreate.
So, to answer your question of scientists' role in an anarchist society, I would say that there is no room for them.