What exactly was the purpose of the JSON config file?
The .elf produced by artiq_compile is the compiled binary of the ARTIQ-Python code you put into it. This can then be directly loaded onto and executed by your core device, which normally only done for idle and startup kernels. For regular experiments the intended workflow is to use artiq_run or the management system, which will call the compiler and communicate with the core device as necessary for a given experiment. Various configuration files (the system description file, the device database, etc.) are used when setting up different ARTIQ components but these don't describe experiments.
In terms of not starting from zero, if you prefer not to write your Python manually, you might also look into a table-format GUI recently developed by members of this community, called Quantrol. Is that anything like what you're looking for?