A little surface rust is not a concern. Just clean the metal with some sort of abrasive material in the joint area before you try to join/braze anything.
After the frame is finished, a good soak in a phosphate solution is a good idea. It will get rid of that rust and leave a coating on the frame which will provide a little protection from future rust and give the paint a good surface to adhere to. Autobody shops sell phosphate solution, often called metal conditioner, as well as many hardware stores.